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GermlineCNVCaller different results with same GATK and different Ubuntu #8619

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Stikus opened this issue Dec 12, 2023 · 2 comments
Closed
1 task done

GermlineCNVCaller different results with same GATK and different Ubuntu #8619

Stikus opened this issue Dec 12, 2023 · 2 comments

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@Stikus
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Stikus commented Dec 12, 2023 •
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Bug Report

Affected tool(s) or class(es)

GermlineCNVCaller

Affected version(s)

  • Latest public release version [4.3.0.0 and 4.4.0.0]

Description

GermlineCNVCaller pipeline provide different results with same GATK version (4.3.0.0) on different base Ubuntu images (18.04 and 22.04). Test results of GATK version 4.3.0.0 and 4.4.0.0 are same on Ubuntu 22.04 - I assume there are no changes in GermlineCNVCaller between 4.3.0.0 and 4.4.0.0.

Steps to reproduce

Command list:

/soft/gatk-4.3.0.0/gatk PreprocessIntervals -R /ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --padding 0 -L chr1:10000-35000 -L chr22:198477-20003000  -imr OVERLAPPING_ONLY -O /outputs/gatk_intervals.interval_list

/soft/gatk-4.3.0.0/gatk AnnotateIntervals -L /outputs/gatk_intervals.interval_list -R /ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa -imr OVERLAPPING_ONLY -O /outputs/gatk_intervals.interval_list.annotated.tsv

/soft/gatk-4.3.0.0/gatk CollectReadCounts -I /inputs/E07002_normal_alignment.bam -R /ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa -L /outputs/gatk_intervals.interval_list --interval-merging-rule OVERLAPPING_ONLY -O /outputs/E07002_normal_alignment.bam.counts.hdf5
/soft/gatk-4.3.0.0/gatk CollectReadCounts -I /inputs/E07002_tumor_alignment.bam -R /ref/GRCh38.d1.vd1/GRCh38.d1.vd1.fa -L /outputs/gatk_intervals.interval_list --interval-merging-rule OVERLAPPING_ONLY -O /outputs/E07002_tumor_alignment.bam.counts.hdf5

/soft/gatk-4.3.0.0/gatk DetermineGermlineContigPloidy -L /outputs/gatk_intervals.interval_list --interval-merging-rule OVERLAPPING_ONLY --contig-ploidy-priors /outputs/a_valid_ploidy_priors_table.tsv.copy.tsv --output /outputs/COHORT_runDir --output-prefix COHORT --input /outputs/E07002_normal_alignment.bam.counts.hdf5 --input /outputs/E07002_tumor_alignment.bam.counts.hdf5

/soft/gatk-4.3.0.0/gatk GermlineCNVCaller --run-mode COHORT -L /outputs/gatk_intervals.interval_list --interval-merging-rule OVERLAPPING_ONLY --annotated-intervals /outputs/gatk_intervals.interval_list.annotated.tsv --contig-ploidy-calls /outputs/COHORT_runDir/COHORT-calls --input /outputs/E07002_normal_alignment.bam.counts.hdf5 --input /outputs/E07002_tumor_alignment.bam.counts.hdf5  --output /outputs/COHORT_runDir --output-prefix COHORT

We used data from PRJNA399748 project to test.

Expected behavior

  • test_gatkgermlinecnvcaller_genotyped-intervals-cohort_0.woTimestamp.vcf (##contig cut from header and only first 5 chr22 CNVs present)
##fileformat=VCFv4.2
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number maximum a posteriori value">
##FORMAT=<ID=CNLP,Number=.,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
##FORMAT=<ID=CNQ,Number=1,Type=Integer,Description="Genotype call quality as the difference between the best and second best phred-scaled log posterior scores">
##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">
##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>
...
##contig=<ID=HPV-mSD2,length=7300,assembly=GRCh38.d1.vd1>
##source=PostprocessGermlineCNVCalls
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	E07002_normal
chr1	10000	CNV_chr1_10000_10999	N	<DEL>,<DUP>	.	.	END=10999	GT:CN:CNLP:CNQ	1:0:0,80,90,100,108,116:80
chr1	11000	CNV_chr1_11000_11999	N	<DEL>,<DUP>	.	.	END=11999	GT:CN:CNLP:CNQ	1:0:0,81,86,89,92,95:81
chr1	12000	CNV_chr1_12000_12999	N	<DEL>,<DUP>	.	.	END=12999	GT:CN:CNLP:CNQ	1:0:0,93,107,119,129,137:93
chr1	13000	CNV_chr1_13000_13999	N	<DEL>,<DUP>	.	.	END=13999	GT:CN:CNLP:CNQ	1:0:0,89,95,99,102,104:89
chr1	14000	CNV_chr1_14000_14999	N	<DEL>,<DUP>	.	.	END=14999	GT:CN:CNLP:CNQ	1:0:0,86,91,93,96,97:86
chr1	15000	CNV_chr1_15000_15999	N	<DEL>,<DUP>	.	.	END=15999	GT:CN:CNLP:CNQ	1:0:0,82,88,92,97,101:82
chr1	16000	CNV_chr1_16000_16999	N	<DEL>,<DUP>	.	.	END=16999	GT:CN:CNLP:CNQ	1:0:0,80,83,85,86,88:80
chr1	17000	CNV_chr1_17000_17999	N	<DEL>,<DUP>	.	.	END=17999	GT:CN:CNLP:CNQ	1:0:0,85,95,102,109,114:85
chr1	18000	CNV_chr1_18000_18999	N	<DEL>,<DUP>	.	.	END=18999	GT:CN:CNLP:CNQ	1:0:0,80,84,87,90,92:80
chr1	19000	CNV_chr1_19000_19999	N	<DEL>,<DUP>	.	.	END=19999	GT:CN:CNLP:CNQ	1:0:0,79,82,84,87,88:79
chr1	20000	CNV_chr1_20000_20999	N	<DEL>,<DUP>	.	.	END=20999	GT:CN:CNLP:CNQ	1:0:0,82,87,89,92,93:82
chr1	21000	CNV_chr1_21000_21999	N	<DEL>,<DUP>	.	.	END=21999	GT:CN:CNLP:CNQ	1:0:0,82,87,91,94,96:82
chr1	22000	CNV_chr1_22000_22999	N	<DEL>,<DUP>	.	.	END=22999	GT:CN:CNLP:CNQ	1:0:0,84,90,94,97,100:84
chr1	23000	CNV_chr1_23000_23999	N	<DEL>,<DUP>	.	.	END=23999	GT:CN:CNLP:CNQ	1:0:0,82,89,95,99,103:82
chr1	24000	CNV_chr1_24000_24999	N	<DEL>,<DUP>	.	.	END=24999	GT:CN:CNLP:CNQ	1:0:0,80,86,91,95,98:80
chr1	25000	CNV_chr1_25000_25999	N	<DEL>,<DUP>	.	.	END=25999	GT:CN:CNLP:CNQ	1:0:0,77,82,85,87,89:77
chr1	26000	CNV_chr1_26000_26999	N	<DEL>,<DUP>	.	.	END=26999	GT:CN:CNLP:CNQ	1:0:0,76,80,83,85,87:76
chr1	27000	CNV_chr1_27000_27999	N	<DEL>,<DUP>	.	.	END=27999	GT:CN:CNLP:CNQ	1:0:0,76,79,81,83,85:76
chr1	28000	CNV_chr1_28000_28999	N	<DEL>,<DUP>	.	.	END=28999	GT:CN:CNLP:CNQ	1:0:0,77,80,81,83,84:77
chr1	29000	CNV_chr1_29000_29999	N	<DEL>,<DUP>	.	.	END=29999	GT:CN:CNLP:CNQ	1:0:0,133,171,201,227,249:133
chr1	30000	CNV_chr1_30000_30999	N	<DEL>,<DUP>	.	.	END=30999	GT:CN:CNLP:CNQ	1:0:0,80,84,86,89,91:80
chr1	31000	CNV_chr1_31000_31999	N	<DEL>,<DUP>	.	.	END=31999	GT:CN:CNLP:CNQ	1:0:0,79,82,85,87,88:79
chr1	32000	CNV_chr1_32000_32999	N	<DEL>,<DUP>	.	.	END=32999	GT:CN:CNLP:CNQ	1:0:0,80,85,89,93,96:80
chr1	33000	CNV_chr1_33000_33999	N	<DEL>,<DUP>	.	.	END=33999	GT:CN:CNLP:CNQ	1:0:0,79,82,84,86,87:79
chr1	34000	CNV_chr1_34000_34999	N	<DEL>,<DUP>	.	.	END=34999	GT:CN:CNLP:CNQ	1:0:0,83,87,90,92,95:83
chr1	35000	CNV_chr1_35000_35000	N	<DEL>,<DUP>	.	.	END=35000	GT:CN:CNLP:CNQ	1:0:0,358,494,595,676,746:358
chr22	10509477	CNV_chr22_10509477_10510476	N	<DEL>,<DUP>	.	.	END=10510476	GT:CN:CNLP:CNQ	1:0:0,20,21,21,22,23:20
chr22	10510477	CNV_chr22_10510477_10511476	N	<DEL>,<DUP>	.	.	END=10511476	GT:CN:CNLP:CNQ	1:0:0,179,247,299,342,380:179
chr22	10511477	CNV_chr22_10511477_10512476	N	<DEL>,<DUP>	.	.	END=10512476	GT:CN:CNLP:CNQ	1:0:0,52,50,59,62,64:50
chr22	10512477	CNV_chr22_10512477_10513476	N	<DEL>,<DUP>	.	.	END=10513476	GT:CN:CNLP:CNQ	1:0:0,170,225,283,324,360:170
chr22	10513477	CNV_chr22_10513477_10514476	N	<DEL>,<DUP>	.	.	END=10514476	GT:CN:CNLP:CNQ	1:0:0,107,122,157,177,195:107
  • test_gatkgermlinecnvcaller_genotyped-segments-cohort_0.woTimestamp.vcf (##contig cut from header)
##fileformat=VCFv4.2
##FILTER=<ID=FREQ,Description="Depth-only copy number record whose AF value is higher than user specified threshold">
##FILTER=<ID=LOW_QS,Description="Depth-only copy number record whose QS value is lower than user specified threshold">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Segment most-likely copy-number call">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Segment genotype">
##FORMAT=<ID=NP,Number=1,Type=Integer,Description="Number of points (i.e. targets or bins) in the segment">
##FORMAT=<ID=QA,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that all points (i.e. targets or bins) in the segment agree with the segment copy-number call">
##FORMAT=<ID=QS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that at least one point (i.e. target or bin) in the segment agrees with the segment copy-number call">
##FORMAT=<ID=QSE,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that the segment end position is a genuine copy-number changepoint">
##FORMAT=<ID=QSS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that the segment start position is a genuine copy-number changepoint">
##INFO=<ID=AC_Orig,Number=A,Type=Integer,Description="Original AC">
##INFO=<ID=AF_Orig,Number=A,Type=Float,Description="Original AF">
##INFO=<ID=AN_Orig,Number=1,Type=Integer,Description="Original AN">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>
...
##contig=<ID=HPV-mSD2,length=7300,assembly=GRCh38.d1.vd1>
##gcnvVcfSchemaVersion=2.0
##source=PostprocessGermlineCNVCalls
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	E07002_normal
chr1	10000	CNV_chr1_10000_35000	N	<DEL>	544.75	.	END=35000	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:26:64:545:358:80
chr22	10509477	CNV_chr22_10509477_10679476	N	<DEL>	3076.53	.	END=10679476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:170:1:3077:1:15
chr22	10679477	CNV_chr22_10679477_10681476	N	<DUP>	34.23	.	END=10681476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:2:19:34:1:1
chr22	10681477	CNV_chr22_10681477_10730476	N	<DEL>	1898.83	.	END=10730476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:49:0:1899:1:1
chr22	10730477	CNV_chr22_10730477_10753476	N	<DUP>	35.09	.	END=10753476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:23:1:35:1:1
chr22	10753477	CNV_chr22_10753477_10775476	N	<DEL>	565.03	.	END=10775476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:22:1:565:2:1
chr22	10775477	CNV_chr22_10775477_10785476	N	<DUP>	3.32	.	END=10785476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:10:1:3:12:1
chr22	10834477	CNV_chr22_10834477_10967476	N	<DEL>	3076.53	.	END=10967476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:84:1:3077:2:12
chr22	11016477	CNV_chr22_11016477_11069476	N	.	17.18	.	END=11069476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:53:0:17:14:0
chr22	11118477	CNV_chr22_11118477_11278476	N	<DEL>	2924.73	.	END=11278476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:111:1:2925:1:14
chr22	11278477	CNV_chr22_11278477_11281476	N	.	54.23	.	END=11281476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:3:28:54:1:1
chr22	11281477	CNV_chr22_11281477_11491476	N	<DEL>	1797.32	.	END=11491476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:161:0:1797:1:1
chr22	11491477	CNV_chr22_11491477_11497476	N	<DUP>	2.95	.	END=11497476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:6:1:3:5:0
chr22	11546477	CNV_chr22_11546477_11572476	N	<DEL>	408.10	.	END=11572476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:26:1:408:1:7
chr22	11572477	CNV_chr22_11572477_11577476	N	.	15.88	.	END=11577476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:5:5:16:1:1
chr22	11577477	CNV_chr22_11577477_11601476	N	<DEL>	274.99	.	END=11601476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:24:0:275:1:1
chr22	11601477	CNV_chr22_11601477_11631476	N	<DUP>	224	.	END=11631476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:30:1:224:5:1
chr22	11680477	CNV_chr22_11680477_15623476	N	<DEL>	3076.53	.	END=15623476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:1352:0:3077:1:9
chr22	15623477	CNV_chr22_15623477_15632476	N	<DUP>	173.15	.	END=15632476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:9:8:173:1:1
chr22	15632477	CNV_chr22_15632477_16422476	N	<DEL>	3076.53	.	END=16422476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:768:0:3077:1:1
chr22	16422477	CNV_chr22_16422477_16428476	N	<DUP>	137.11	.	END=16428476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:6:8:137:6:1
chr22	16428477	CNV_chr22_16428477_16463476	N	<DEL>	578.32	.	END=16463476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:35:1:578:1:6
chr22	16463477	CNV_chr22_16463477_16465476	N	.	26.80	.	END=16465476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:2:23:27:1:1
chr22	16465477	CNV_chr22_16465477_16553476	N	<DEL>	2052.12	.	END=16553476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:88:0:2052:1:1
chr22	16553477	CNV_chr22_16553477_16554476	N	.	8.59	.	END=16554476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:1:9:9:9:9
chr22	16554477	CNV_chr22_16554477_16571476	N	<DEL>	669.23	.	END=16571476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:17:1:669:3:1
chr22	16571477	CNV_chr22_16571477_16610476	N	<DUP>	201.07	.	END=16610476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:39:1:201:1:3
chr22	16610477	CNV_chr22_16610477_16638476	N	<DEL>	389.92	.	END=16638476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:28:0:390:1:1
chr22	16638477	CNV_chr22_16638477_16639476	N	<DUP>	4.82	.	END=16639476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:5:5:5:5
chr22	16639477	CNV_chr22_16639477_16751476	N	<DEL>	3076.53	.	END=16751476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:112:0:3077:1:1
chr22	16751477	CNV_chr22_16751477_16752476	N	<DUP>	1.99	.	END=16752476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:1:2:2:2:2
chr22	16752477	CNV_chr22_16752477_16861476	N	<DEL>	3028.23	.	END=16861476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:109:0:3028:1:1
chr22	16861477	CNV_chr22_16861477_16866476	N	.	22.74	.	END=16866476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:5:3:23:1:1
chr22	16866477	CNV_chr22_16866477_16935476	N	<DEL>	663.59	.	END=16935476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:69:0:664:1:1
chr22	16935477	CNV_chr22_16935477_16958476	N	.	15.11	.	END=16958476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:23:2:15:1:0
chr22	16958477	CNV_chr22_16958477_17038476	N	<DEL>	870.48	.	END=17038476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:80:0:870:1:1
chr22	17038477	CNV_chr22_17038477_17039476	N	<DUP>	46.58	.	END=17039476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:47:47:47:47
chr22	17039477	CNV_chr22_17039477_17084476	N	<DEL>	128.97	.	END=17084476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:129:1:1
chr22	17084477	CNV_chr22_17084477_17085476	N	<DUP>	2.05	.	END=17085476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:2:2:2:2
chr22	17085477	CNV_chr22_17085477_17120476	N	<DEL>	206.56	.	END=17120476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:35:0:207:1:2
chr22	17120477	CNV_chr22_17120477_17153476	N	<DEL>	8.93	.	END=17153476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:33:1:9:1:1
chr22	17153477	CNV_chr22_17153477_17254476	N	<DEL>	517.31	.	END=17254476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:101:0:517:1:1
chr22	17254477	CNV_chr22_17254477_17259476	N	<DUP>	2.11	.	END=17259476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:5:1:2:1:0
chr22	17259477	CNV_chr22_17259477_17336476	N	<DEL>	161.25	.	END=17336476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:77:0:161:0:1
chr22	17336477	CNV_chr22_17336477_17388476	N	<DUP>	17.85	.	END=17388476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:52:0:18:1:1
chr22	17388477	CNV_chr22_17388477_17438476	N	<DEL>	70.16	.	END=17438476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:50:1:70:2:1
chr22	17438477	CNV_chr22_17438477_17439476	N	<DUP>	1.34	.	END=17439476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:1:1:1:1
chr22	17439477	CNV_chr22_17439477_17516476	N	<DEL>	181.14	.	END=17516476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:77:0:181:1:1
chr22	17516477	CNV_chr22_17516477_17519476	N	<DUP>	1.59	.	END=17519476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:3:1:2:1:0
chr22	17519477	CNV_chr22_17519477_17564476	N	<DEL>	60.18	.	END=17564476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:60:1:1
chr22	17564477	CNV_chr22_17564477_17565476	N	<DUP>	1.77	.	END=17565476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:2:2:2:2
chr22	17565477	CNV_chr22_17565477_17773476	N	<DEL>	1065.58	.	END=17773476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:208:0:1066:1:1
chr22	17773477	CNV_chr22_17773477_17791476	N	<DEL>	5.44	.	END=17791476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:18:1:5:1:0
chr22	17791477	CNV_chr22_17791477_17825476	N	<DEL>	136.29	.	END=17825476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:34:1:136:1:1
chr22	17825477	CNV_chr22_17825477_17833476	N	<DUP>	5.28	.	END=17833476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:8:2:5:1:1
chr22	17833477	CNV_chr22_17833477_17908476	N	<DEL>	219.96	.	END=17908476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:75:0:220:1:1
chr22	17908477	CNV_chr22_17908477_17909476	N	<DUP>	2.24	.	END=17909476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:2:2:2:2
chr22	17909477	CNV_chr22_17909477_17996476	N	<DEL>	237.23	.	END=17996476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:87:0:237:1:1
chr22	17996477	CNV_chr22_17996477_18009476	N	<DUP>	4.45	.	END=18009476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:13:1:4:1:1
chr22	18009477	CNV_chr22_18009477_18119476	N	<DEL>	503.55	.	END=18119476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:110:0:504:1:1
chr22	18119477	CNV_chr22_18119477_18120476	N	<DUP>	2.71	.	END=18120476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:3:3:3:3
chr22	18120477	CNV_chr22_18120477_18155476	N	<DEL>	159.28	.	END=18155476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:35:0:159:1:1
chr22	18155477	CNV_chr22_18155477_18171476	N	<DUP>	3.10	.	END=18171476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:16:0:3:1:0
chr22	18171477	CNV_chr22_18171477_18622476	N	<DEL>	3076.53	.	END=18622476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:303:0:3077:1:1
chr22	18622477	CNV_chr22_18622477_18625476	N	<DUP>	95.54	.	END=18625476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:3:28:96:2:1
chr22	18625477	CNV_chr22_18625477_18852476	N	<DEL>	3076.53	.	END=18852476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:178:0:3077:2:1
chr22	18852477	CNV_chr22_18852477_18905476	N	.	196.14	.	END=18905476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:53:26:196:2:2
chr22	18905477	CNV_chr22_18905477_18954476	N	<DEL>	449.27	.	END=18954476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:49:0:449:1:1
chr22	18954477	CNV_chr22_18954477_18962476	N	.	19.45	.	END=18962476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:8:4:19:1:1
chr22	18962477	CNV_chr22_18962477_19067476	N	<DEL>	475.37	.	END=19067476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:105:0:475:0:1
chr22	19067477	CNV_chr22_19067477_19068476	N	.	44.94	.	END=19068476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:1:45:45:45:45
chr22	19068477	CNV_chr22_19068477_19107476	N	<DEL>	33.71	.	END=19107476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:39:0:34:0:1
chr22	19107477	CNV_chr22_19107477_19123476	N	<DUP>	3.81	.	END=19123476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:16:1:4:1:0
chr22	19123477	CNV_chr22_19123477_19193476	N	<DEL>	995.35	.	END=19193476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:70:0:995:1:1
chr22	19193477	CNV_chr22_19193477_19207476	N	<DUP>	3.96	.	END=19207476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:14:1:4:1:1
chr22	19207477	CNV_chr22_19207477_19287476	N	<DEL>	209.67	.	END=19287476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:80:0:210:1:1
chr22	19287477	CNV_chr22_19287477_19292476	N	.	71.36	.	END=19292476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:5:16:71:1:1
chr22	19292477	CNV_chr22_19292477_19336476	N	<DEL>	11.69	.	END=19336476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:44:0:12:0:0
chr22	19336477	CNV_chr22_19336477_19337476	N	<DUP>	6.13	.	END=19337476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:6:6:6:6
chr22	19337477	CNV_chr22_19337477_19388476	N	<DEL>	110.41	.	END=19388476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:51:0:110:1:0
chr22	19388477	CNV_chr22_19388477_19496476	N	.	31.22	.	END=19496476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:108:0:31:1:0
chr22	19496477	CNV_chr22_19496477_19676476	N	<DEL>	1068.34	.	END=19676476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:180:0:1068:1:1
chr22	19676477	CNV_chr22_19676477_19677476	N	<DUP>	2.06	.	END=19677476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:2:2:2:2
chr22	19677477	CNV_chr22_19677477_19722476	N	<DEL>	608.09	.	END=19722476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:608:3:1
chr22	19722477	CNV_chr22_19722477_19727476	N	<DUP>	3.21	.	END=19727476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:5:2:3:2:1
chr22	19727477	CNV_chr22_19727477_19748476	N	<DEL>	21.05	.	END=19748476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:21:0:21:1:2
chr22	19748477	CNV_chr22_19748477_19759476	N	<DEL>	15.41	.	END=19759476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:11:8:15:3:1
chr22	19759477	CNV_chr22_19759477_19823476	N	<DEL>	521.94	.	END=19823476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:64:0:522:2:3
chr22	19823477	CNV_chr22_19823477_19851476	N	.	5.86	.	END=19851476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:28:1:6:1:1
chr22	19851477	CNV_chr22_19851477_19895476	N	<DEL>	643.95	.	END=19895476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:44:1:644:1:1
chr22	19895477	CNV_chr22_19895477_19901476	N	<DUP>	2.30	.	END=19901476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:6:1:2:1:0
chr22	19901477	CNV_chr22_19901477_19946476	N	<DEL>	123.62	.	END=19946476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:124:1:1
chr22	19946477	CNV_chr22_19946477_19971476	N	<DUP>	6.86	.	END=19971476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:25:0:7:2:1
chr22	19971477	CNV_chr22_19971477_20003000	N	<DEL>	198.68	.	END=20003000	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:32:0:199:2:2

Actual behavior

  • gatkgermlinecnvcaller_genotyped-intervals-COHORT_0.woTimestamp.vcf (##contig cut from header and only first 5 chr22 CNVs present)
##fileformat=VCFv4.2
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number maximum a posteriori value">
##FORMAT=<ID=CNLP,Number=.,Type=Integer,Description="Copy number log posterior (in Phred-scale) rounded down">
##FORMAT=<ID=CNQ,Number=1,Type=Integer,Description="Genotype call quality as the difference between the best and second best phred-scaled log posterior scores">
##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">
##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>
...
##contig=<ID=HPV-mSD2,length=7300,assembly=GRCh38.d1.vd1>
##source=PostprocessGermlineCNVCalls
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	E07002_normal
chr1	10000	CNV_chr1_10000_10999	N	<DEL>,<DUP>	.	.	END=10999	GT:CN:CNLP:CNQ	1:0:0,78,88,96,104,111:78
chr1	11000	CNV_chr1_11000_11999	N	<DEL>,<DUP>	.	.	END=11999	GT:CN:CNLP:CNQ	1:0:0,80,85,88,90,93:80
chr1	12000	CNV_chr1_12000_12999	N	<DEL>,<DUP>	.	.	END=12999	GT:CN:CNLP:CNQ	1:0:0,89,101,110,119,126:89
chr1	13000	CNV_chr1_13000_13999	N	<DEL>,<DUP>	.	.	END=13999	GT:CN:CNLP:CNQ	1:0:0,89,96,101,105,108:89
chr1	14000	CNV_chr1_14000_14999	N	<DEL>,<DUP>	.	.	END=14999	GT:CN:CNLP:CNQ	1:0:0,86,91,94,96,98:86
chr1	15000	CNV_chr1_15000_15999	N	<DEL>,<DUP>	.	.	END=15999	GT:CN:CNLP:CNQ	1:0:0,83,89,94,99,103:83
chr1	16000	CNV_chr1_16000_16999	N	<DEL>,<DUP>	.	.	END=16999	GT:CN:CNLP:CNQ	1:0:0,80,83,85,87,89:80
chr1	17000	CNV_chr1_17000_17999	N	<DEL>,<DUP>	.	.	END=17999	GT:CN:CNLP:CNQ	1:0:0,85,94,101,107,112:85
chr1	18000	CNV_chr1_18000_18999	N	<DEL>,<DUP>	.	.	END=18999	GT:CN:CNLP:CNQ	1:0:0,81,85,89,91,94:81
chr1	19000	CNV_chr1_19000_19999	N	<DEL>,<DUP>	.	.	END=19999	GT:CN:CNLP:CNQ	1:0:0,79,83,85,87,89:79
chr1	20000	CNV_chr1_20000_20999	N	<DEL>,<DUP>	.	.	END=20999	GT:CN:CNLP:CNQ	1:0:0,82,87,89,91,93:82
chr1	21000	CNV_chr1_21000_21999	N	<DEL>,<DUP>	.	.	END=21999	GT:CN:CNLP:CNQ	1:0:0,81,86,90,93,96:81
chr1	22000	CNV_chr1_22000_22999	N	<DEL>,<DUP>	.	.	END=22999	GT:CN:CNLP:CNQ	1:0:0,83,89,94,97,100:83
chr1	23000	CNV_chr1_23000_23999	N	<DEL>,<DUP>	.	.	END=23999	GT:CN:CNLP:CNQ	1:0:0,81,88,92,96,100:81
chr1	24000	CNV_chr1_24000_24999	N	<DEL>,<DUP>	.	.	END=24999	GT:CN:CNLP:CNQ	1:0:0,79,85,90,94,98:79
chr1	25000	CNV_chr1_25000_25999	N	<DEL>,<DUP>	.	.	END=25999	GT:CN:CNLP:CNQ	1:0:0,76,80,83,85,87:76
chr1	26000	CNV_chr1_26000_26999	N	<DEL>,<DUP>	.	.	END=26999	GT:CN:CNLP:CNQ	1:0:0,76,79,82,84,86:76
chr1	27000	CNV_chr1_27000_27999	N	<DEL>,<DUP>	.	.	END=27999	GT:CN:CNLP:CNQ	1:0:0,76,79,82,84,86:76
chr1	28000	CNV_chr1_28000_28999	N	<DEL>,<DUP>	.	.	END=28999	GT:CN:CNLP:CNQ	1:0:0,77,80,82,83,85:77
chr1	29000	CNV_chr1_29000_29999	N	<DEL>,<DUP>	.	.	END=29999	GT:CN:CNLP:CNQ	1:0:0,131,171,202,228,252:131
chr1	30000	CNV_chr1_30000_30999	N	<DEL>,<DUP>	.	.	END=30999	GT:CN:CNLP:CNQ	1:0:0,79,82,84,86,88:79
chr1	31000	CNV_chr1_31000_31999	N	<DEL>,<DUP>	.	.	END=31999	GT:CN:CNLP:CNQ	1:0:0,78,82,84,86,88:78
chr1	32000	CNV_chr1_32000_32999	N	<DEL>,<DUP>	.	.	END=32999	GT:CN:CNLP:CNQ	1:0:0,78,83,87,90,93:78
chr1	33000	CNV_chr1_33000_33999	N	<DEL>,<DUP>	.	.	END=33999	GT:CN:CNLP:CNQ	1:0:0,79,82,84,85,87:79
chr1	34000	CNV_chr1_34000_34999	N	<DEL>,<DUP>	.	.	END=34999	GT:CN:CNLP:CNQ	1:0:0,84,88,91,94,96:84
chr1	35000	CNV_chr1_35000_35000	N	<DEL>,<DUP>	.	.	END=35000	GT:CN:CNLP:CNQ	1:0:0,344,480,580,662,732:344
chr22	10509477	CNV_chr22_10509477_10510476	N	<DEL>,<DUP>	.	.	END=10510476	GT:CN:CNLP:CNQ	1:0:0,20,20,21,22,22:20
chr22	10510477	CNV_chr22_10510477_10511476	N	<DEL>,<DUP>	.	.	END=10511476	GT:CN:CNLP:CNQ	1:0:0,156,226,278,320,356:156
chr22	10511477	CNV_chr22_10511477_10512476	N	<DEL>,<DUP>	.	.	END=10512476	GT:CN:CNLP:CNQ	1:0:0,51,49,57,59,62:49
chr22	10512477	CNV_chr22_10512477_10513476	N	<DEL>,<DUP>	.	.	END=10513476	GT:CN:CNLP:CNQ	1:0:0,186,246,304,344,379:186
chr22	10513477	CNV_chr22_10513477_10514476	N	<DEL>,<DUP>	.	.	END=10514476	GT:CN:CNLP:CNQ	1:0:0,112,130,167,189,209:112
  • gatkgermlinecnvcaller_genotyped-segments-COHORT_0.woTimestamp.vcf (##contig cut from header)
##fileformat=VCFv4.2
##FILTER=<ID=FREQ,Description="Depth-only copy number record whose AF value is higher than user specified threshold">
##FILTER=<ID=LOW_QS,Description="Depth-only copy number record whose QS value is lower than user specified threshold">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Segment most-likely copy-number call">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Segment genotype">
##FORMAT=<ID=NP,Number=1,Type=Integer,Description="Number of points (i.e. targets or bins) in the segment">
##FORMAT=<ID=QA,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that all points (i.e. targets or bins) in the segment agree with the segment copy-number call">
##FORMAT=<ID=QS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that at least one point (i.e. target or bin) in the segment agrees with the segment copy-number call">
##FORMAT=<ID=QSE,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that the segment end position is a genuine copy-number changepoint">
##FORMAT=<ID=QSS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that the segment start position is a genuine copy-number changepoint">
##INFO=<ID=AC_Orig,Number=A,Type=Integer,Description="Original AC">
##INFO=<ID=AF_Orig,Number=A,Type=Float,Description="Original AF">
##INFO=<ID=AN_Orig,Number=1,Type=Integer,Description="Original AN">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##contig=<ID=chr1,length=248956422,assembly=GRCh38.d1.vd1>
...
##contig=<ID=HPV-mSD2,length=7300,assembly=GRCh38.d1.vd1>
##gcnvVcfSchemaVersion=2.0
##source=PostprocessGermlineCNVCalls
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	E07002_normal
chr1	10000	CNV_chr1_10000_35000	N	<DEL>	520.24	.	END=35000	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:26:64:520:344:78
chr22	10509477	CNV_chr22_10509477_10678476	N	<DEL>	3076.53	.	END=10678476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:169:2:3077:1:14
chr22	10678477	CNV_chr22_10678477_10681476	N	<DUP>	36.21	.	END=10681476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:3:6:36:1:1
chr22	10681477	CNV_chr22_10681477_10730476	N	<DEL>	1952.54	.	END=10730476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:49:0:1953:1:1
chr22	10730477	CNV_chr22_10730477_10753476	N	<DUP>	41.10	.	END=10753476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:23:1:41:1:1
chr22	10753477	CNV_chr22_10753477_10775476	N	<DEL>	562.51	.	END=10775476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:22:1:563:1:1
chr22	10775477	CNV_chr22_10775477_10785476	N	<DUP>	3.07	.	END=10785476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:10:1:3:12:0
chr22	10834477	CNV_chr22_10834477_10967476	N	<DEL>	3076.53	.	END=10967476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:84:1:3077:1:12
chr22	11016477	CNV_chr22_11016477_11052476	N	<DEL>	7.47	.	END=11052476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:36:0:7:0:1
chr22	11052477	CNV_chr22_11052477_11069476	N	<DUP>	34.61	.	END=11069476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:17:3:35:14:0
chr22	11118477	CNV_chr22_11118477_11278476	N	<DEL>	2974.76	.	END=11278476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:111:1:2975:1:14
chr22	11278477	CNV_chr22_11278477_11281476	N	<DUP>	32.71	.	END=11281476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:3:24:33:1:1
chr22	11281477	CNV_chr22_11281477_11491476	N	<DEL>	1803.27	.	END=11491476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:161:0:1803:1:1
chr22	11491477	CNV_chr22_11491477_11497476	N	<DUP>	3.22	.	END=11497476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:6:2:3:4:0
chr22	11546477	CNV_chr22_11546477_11572476	N	<DEL>	375.05	.	END=11572476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:26:1:375:1:6
chr22	11572477	CNV_chr22_11572477_11577476	N	.	14.19	.	END=11577476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:5:5:14:1:1
chr22	11577477	CNV_chr22_11577477_11601476	N	<DEL>	278.05	.	END=11601476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:24:0:278:1:1
chr22	11601477	CNV_chr22_11601477_11631476	N	<DUP>	248.94	.	END=11631476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:30:1:249:5:1
chr22	11680477	CNV_chr22_11680477_15623476	N	<DEL>	3076.53	.	END=15623476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:1352:0:3077:1:9
chr22	15623477	CNV_chr22_15623477_15632476	N	<DUP>	234.56	.	END=15632476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:9:8:235:1:1
chr22	15632477	CNV_chr22_15632477_16422476	N	<DEL>	3076.53	.	END=16422476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:768:0:3077:1:1
chr22	16422477	CNV_chr22_16422477_16428476	N	<DUP>	155.83	.	END=16428476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:6:8:156:7:1
chr22	16428477	CNV_chr22_16428477_16463476	N	<DEL>	602.78	.	END=16463476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:35:1:603:1:7
chr22	16463477	CNV_chr22_16463477_16465476	N	.	32.56	.	END=16465476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:2:25:33:1:1
chr22	16465477	CNV_chr22_16465477_16553476	N	<DEL>	2152.01	.	END=16553476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:88:0:2152:1:1
chr22	16553477	CNV_chr22_16553477_16554476	N	<DUP>	4.37	.	END=16554476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:4:4:4:4
chr22	16554477	CNV_chr22_16554477_16571476	N	<DEL>	751.12	.	END=16571476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:17:1:751:4:1
chr22	16571477	CNV_chr22_16571477_16610476	N	<DUP>	272.59	.	END=16610476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:39:1:273:1:4
chr22	16610477	CNV_chr22_16610477_16638476	N	<DEL>	410.77	.	END=16638476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:28:0:411:1:1
chr22	16638477	CNV_chr22_16638477_16639476	N	<DUP>	4.92	.	END=16639476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:5:5:5:5
chr22	16639477	CNV_chr22_16639477_16751476	N	<DEL>	3076.53	.	END=16751476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:112:0:3077:1:1
chr22	16751477	CNV_chr22_16751477_16752476	N	<DUP>	2.09	.	END=16752476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:1:2:2:2:2
chr22	16752477	CNV_chr22_16752477_16861476	N	<DEL>	3014.01	.	END=16861476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:109:0:3014:1:1
chr22	16861477	CNV_chr22_16861477_16866476	N	.	32.90	.	END=16866476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:5:3:33:1:1
chr22	16866477	CNV_chr22_16866477_16935476	N	<DEL>	654.40	.	END=16935476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:69:0:654:1:1
chr22	16935477	CNV_chr22_16935477_16958476	N	<DUP>	8.98	.	END=16958476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:23:1:9:2:0
chr22	16958477	CNV_chr22_16958477_17038476	N	<DEL>	811.16	.	END=17038476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:80:0:811:1:1
chr22	17038477	CNV_chr22_17038477_17039476	N	<DUP>	57.76	.	END=17039476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:58:58:58:58
chr22	17039477	CNV_chr22_17039477_17084476	N	<DEL>	119.14	.	END=17084476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:119:1:1
chr22	17084477	CNV_chr22_17084477_17085476	N	<DUP>	2.02	.	END=17085476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:2:2:2:2
chr22	17085477	CNV_chr22_17085477_17120476	N	<DEL>	205.90	.	END=17120476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:35:0:206:1:1
chr22	17120477	CNV_chr22_17120477_17153476	N	<DEL>	8.78	.	END=17153476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:33:1:9:1:1
chr22	17153477	CNV_chr22_17153477_17254476	N	<DEL>	496.07	.	END=17254476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:101:0:496:1:1
chr22	17254477	CNV_chr22_17254477_17259476	N	<DUP>	2.22	.	END=17259476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:5:1:2:1:0
chr22	17259477	CNV_chr22_17259477_17336476	N	<DEL>	151.74	.	END=17336476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:77:0:152:0:1
chr22	17336477	CNV_chr22_17336477_17388476	N	<DUP>	16.51	.	END=17388476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:52:0:17:1:0
chr22	17388477	CNV_chr22_17388477_17438476	N	<DEL>	64.33	.	END=17438476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:50:0:64:1:1
chr22	17438477	CNV_chr22_17438477_17439476	N	<DUP>	1.36	.	END=17439476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:1:1:1:1
chr22	17439477	CNV_chr22_17439477_17516476	N	<DEL>	181.65	.	END=17516476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:77:0:182:1:1
chr22	17516477	CNV_chr22_17516477_17519476	N	<DUP>	1.34	.	END=17519476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:3:1:1:1:0
chr22	17519477	CNV_chr22_17519477_17564476	N	<DEL>	54.24	.	END=17564476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:54:1:1
chr22	17564477	CNV_chr22_17564477_17565476	N	<DUP>	1.78	.	END=17565476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:2:2:2:2
chr22	17565477	CNV_chr22_17565477_17773476	N	<DEL>	1064.67	.	END=17773476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:208:0:1065:1:1
chr22	17773477	CNV_chr22_17773477_17791476	N	<DEL>	5.48	.	END=17791476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:18:1:5:1:0
chr22	17791477	CNV_chr22_17791477_17825476	N	<DEL>	142.12	.	END=17825476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:34:0:142:1:1
chr22	17825477	CNV_chr22_17825477_17833476	N	<DUP>	3.77	.	END=17833476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:8:2:4:1:1
chr22	17833477	CNV_chr22_17833477_17908476	N	<DEL>	194.02	.	END=17908476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:75:0:194:1:1
chr22	17908477	CNV_chr22_17908477_17909476	N	<DUP>	2.44	.	END=17909476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:1:2:2:2:2
chr22	17909477	CNV_chr22_17909477_17996476	N	<DEL>	223.01	.	END=17996476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:87:0:223:1:1
chr22	17996477	CNV_chr22_17996477_18009476	N	<DUP>	4.11	.	END=18009476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:13:1:4:1:1
chr22	18009477	CNV_chr22_18009477_18119476	N	<DEL>	462.71	.	END=18119476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:110:0:463:1:1
chr22	18119477	CNV_chr22_18119477_18120476	N	<DUP>	3.08	.	END=18120476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:1:3:3:3:3
chr22	18120477	CNV_chr22_18120477_18155476	N	<DEL>	181.69	.	END=18155476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:35:0:182:1:1
chr22	18155477	CNV_chr22_18155477_18171476	N	<DUP>	3.28	.	END=18171476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:16:1:3:1:0
chr22	18171477	CNV_chr22_18171477_18622476	N	<DEL>	3076.53	.	END=18622476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:303:0:3077:1:1
chr22	18622477	CNV_chr22_18622477_18625476	N	<DUP>	108.43	.	END=18625476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:3:28:108:2:1
chr22	18625477	CNV_chr22_18625477_18851476	N	<DEL>	3076.53	.	END=18851476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:177:1:3077:2:1
chr22	18851477	CNV_chr22_18851477_18905476	N	.	204.20	.	END=18905476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:54:4:204:1:2
chr22	18905477	CNV_chr22_18905477_18954476	N	<DEL>	444.58	.	END=18954476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:49:0:445:1:1
chr22	18954477	CNV_chr22_18954477_18962476	N	.	17.70	.	END=18962476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:8:5:18:1:1
chr22	18962477	CNV_chr22_18962477_19067476	N	<DEL>	481.71	.	END=19067476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:105:0:482:0:1
chr22	19067477	CNV_chr22_19067477_19068476	N	.	39.64	.	END=19068476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:1:40:40:40:40
chr22	19068477	CNV_chr22_19068477_19100476	N	<DEL>	34.27	.	END=19100476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:32:0:34:1:1
chr22	19100477	CNV_chr22_19100477_19123476	N	<DUP>	4.17	.	END=19123476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:23:0:4:1:0
chr22	19123477	CNV_chr22_19123477_19193476	N	<DEL>	1131.55	.	END=19193476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:70:0:1132:1:1
chr22	19193477	CNV_chr22_19193477_19207476	N	<DUP>	3.79	.	END=19207476	GT:CN:NP:QA:QS:QSE:QSS	./.:4:14:1:4:1:1
chr22	19207477	CNV_chr22_19207477_19287476	N	<DEL>	208.73	.	END=19287476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:80:0:209:1:1
chr22	19287477	CNV_chr22_19287477_19292476	N	.	78.26	.	END=19292476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:5:17:78:1:1
chr22	19292477	CNV_chr22_19292477_19336476	N	<DEL>	15.38	.	END=19336476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:44:0:15:0:0
chr22	19336477	CNV_chr22_19336477_19337476	N	<DUP>	8.68	.	END=19337476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:1:9:9:9:9
chr22	19337477	CNV_chr22_19337477_19388476	N	<DEL>	169.49	.	END=19388476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:51:0:169:1:0
chr22	19388477	CNV_chr22_19388477_19496476	N	.	38.34	.	END=19496476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:108:0:38:1:0
chr22	19496477	CNV_chr22_19496477_19676476	N	<DEL>	1019.30	.	END=19676476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:180:0:1019:1:1
chr22	19676477	CNV_chr22_19676477_19677476	N	<DUP>	1.75	.	END=19677476	GT:CN:NP:QA:QS:QSE:QSS	./.:5:1:2:2:2:2
chr22	19677477	CNV_chr22_19677477_19722476	N	<DEL>	652.97	.	END=19722476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:653:3:1
chr22	19722477	CNV_chr22_19722477_19727476	N	<DUP>	3.28	.	END=19727476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:5:2:3:2:1
chr22	19727477	CNV_chr22_19727477_19748476	N	<DEL>	71.75	.	END=19748476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:21:0:72:1:2
chr22	19748477	CNV_chr22_19748477_19759476	N	<DEL>	12.45	.	END=19759476	GT:CN:NP:QA:QS:QSE:QSS	0/1:1:11:6:12:3:1
chr22	19759477	CNV_chr22_19759477_19823476	N	<DEL>	686.96	.	END=19823476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:64:0:687:2:3
chr22	19823477	CNV_chr22_19823477_19851476	N	.	6.24	.	END=19851476	GT:CN:NP:QA:QS:QSE:QSS	0/0:2:28:1:6:1:1
chr22	19851477	CNV_chr22_19851477_19895476	N	<DEL>	688.75	.	END=19895476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:44:1:689:1:1
chr22	19895477	CNV_chr22_19895477_19901476	N	<DUP>	2.39	.	END=19901476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:6:1:2:1:0
chr22	19901477	CNV_chr22_19901477_19946476	N	<DEL>	114.12	.	END=19946476	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:45:0:114:1:1
chr22	19946477	CNV_chr22_19946477_19971476	N	<DUP>	4.69	.	END=19971476	GT:CN:NP:QA:QS:QSE:QSS	./.:3:25:0:5:2:0
chr22	19971477	CNV_chr22_19971477_20003000	N	<DEL>	96.55	.	END=20003000	GT:CN:NP:QA:QS:QSE:QSS	1/1:0:32:0:97:2:2
@Stikus
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Stikus commented Dec 12, 2023

Here are the differences visualized:

  • test_gatkgermlinecnvcaller_genotyped-intervals-cohort_0.woTimestamp.vcf (Ubuntu 18.04) and gatkgermlinecnvcaller_genotyped-intervals-COHORT_0.woTimestamp.vcf (Ubuntu 22.04)

image

  • test_gatkgermlinecnvcaller_genotyped-segments-cohort_0.woTimestamp.vcf (Ubuntu 18.04) and gatkgermlinecnvcaller_genotyped-segments-COHORT_0.woTimestamp.vcf (Ubuntu 22.04)

image

I assume that some system packages are different (a lot, of course) and causing these differences, but I don't think that it is intended. We are using conda env - so differences in Python should not affect this.

@samuelklee
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samuelklee commented Dec 12, 2023 •
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Thanks also for this detailed report, @Stikus! The differences look small to me (mostly in the quals, which are the result of more numerically sensitive calculations), with the discrepant calls primarily being of low quality.

Since the gCNV python code depends on native C/C++ code (via numpy, theano, etc.), these sorts of floating-point numerical differences might not be unexpected if there are changes in the underlying system packages or hardware. Unfortunately, we can only guarantee numerical reproducibility to this high degree within our Docker testing environment.

Note also the upcoming #8561, which will also introduce changes on this level.

@Stikus Stikus mentioned this issue Dec 14, 2023
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