GT integrate

Open Hanjunmin opened this issue 1 year ago • 1 comments

Hi: I want to ask this: before: chr1 744867 . g GTATATATATATATATA . . . GT ./. 1/. chr1 744867 . g GTATATATATATATATATA . . . GT 1/. ./.

truvari collapse -s 0 -S 50 -p 0.7 -P 0.7 -i "sort"$file".gz" -o "./truvarimerge/${file}_merge.vcf" -c "./truvarimerge/${file}_collapsed.vcf" -f "/home/jmhan/SDR/genome/GRCh38/GCF_000001405.26_GRCh38_genomic.chrNames.fna"

${file}_merge.vcf: chr1 744867 . g GTATATATATATATATATA . . NumCollapsed=1;NumConsolidated=0;CollapseId=15.0 GT 1/. ./.

why this phenotype isn't chr1 744867 . g GTATATATATATATATATA . . NumCollapsed=1;NumConsolidated=0;CollapseId=15.0 GT 1/. 1/.

Thank you !

Mar 14 '24 08:03 Hanjunmin

I believe what's happening here is that because they're partial missing genotypes (the . in ./1), the calls are going through a branch of the code that isn't consolidating the genotypes. A short term solution would be to alter the VCF so that it fills in . with 0. A long term solution will be for me to revisit the genotype handling logic.

Mar 14 '24 13:03 ACEnglish