Rc remove ad from vat #7832
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Rc remove ad from vat #7832
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RoriCremer
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Codecov Report
@@ Coverage Diff @@
## ah_var_store #7832 +/- ##
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Coverage ? 86.303%
Complexity ? 35194
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Files ? 2170
Lines ? 164837
Branches ? 17774
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Hits ? 142260
Misses ? 16254
Partials ? 6323 |
kcibul
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May 5, 2022
gbggrant
approved these changes
May 5, 2022
| @@ -147,9 +147,9 @@ task ExtractAnAcAfFromVCF { | |||
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| ## During normalization, sometimes duplicate variants appear but with different calculations. This seems to be a bug in bcftools. For now we are dropping all duplicate variants | |||
| ## to locate the duplicates, we first make a file of just the first 5 columns | |||
| bcftools query normalized.filtered.bcf -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\n' | sort check_duplicates.tsv | uniq -d | cut -f1,2,3,4,5 > duplicates.tsv | |||
| grep -v '^#' normalized.filtered.bcf | cut -f1,2,4,5 | sort | uniq -d > duplicates.tsv | |||
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You should update the comment on line 149 to indicate that it's not the first 5 columns (using 1,2,4,5)
This was referenced Mar 17, 2023
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