-
Notifications
You must be signed in to change notification settings - Fork 586
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Fix to long deletions that overhang into the assembly window causing …
…exceptions in HaplotypeCaller (#8731)
- Loading branch information
1 parent
2640404
commit 8ee86e7
Showing
4 changed files
with
32 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
29 changes: 29 additions & 0 deletions
29
...tools/haplotypecaller/testGenotypeGivenAllelesMode_givenAlleles_ExtremeLengthDeletion.vcf
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,29 @@ | ||
##fileformat=VCFv4.2 | ||
##FILTER=<ID=LowQual,Description="Low quality"> | ||
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | ||
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> | ||
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | ||
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | ||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> | ||
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> | ||
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> | ||
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> | ||
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> | ||
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> | ||
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation"> | ||
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed"> | ||
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed"> | ||
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> | ||
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> | ||
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> | ||
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality"> | ||
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> | ||
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> | ||
##contig=<ID=20,length=63025520> | ||
##contig=<ID=21,length=48129895> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 | ||
20 10000694 . GAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAA A . . . GT 0|1 |
Binary file added
BIN
+359 Bytes
...s/haplotypecaller/testGenotypeGivenAllelesMode_givenAlleles_ExtremeLengthDeletion.vcf.idx
Binary file not shown.