Closed vondant closed 1 month ago
Yes it can. If you read the VCF format specifications, you'll see they don't change much between versions. But more importantly, by not using a custom VCF parser but instead relying on the pysam library, efficient parsing between specifications is more about pysam having a consistent api than the vcf format specificatio remaining unchanged.
Thanks for the prompt reply!
Following on the same when I tried merging outputs from DELLY, LUMPY and MANTA using Truvari it gave me 2 Variants at the same position for a chromosome.
I used bcftools merge -m none
to remove multi-allelic entries and then ran truvari collapse
with the default parameters and no flags.
chr2 48330378 MantaDUP:TANDEM:24728:0:1:0:0:0 T <DUP:TANDEM> . PASS END=48330518;SVTYPE=DUP;SVLEN=140;SVINSLEN=3;SVINSSEQ=TTG;SOMATIC;SOMATICSCORE=42 PR:SR .:. .:. 40,0:49,0 32,1:56,8
chr2 48330378 DUP00000135 T <DUP> 480 PASS PRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.2.6;END=48330519;PE=0;MAPQ=0;CT=5to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=0;HOMLEN=2;SR=8;SRQ=0.984496;CONSENSUS=GACATTTCTTTTTCTATGAAAAACATTGTTTAGTGATCTGAATTCAGTGAATGACTACCTCTTTCTCTTTATTGAATTGCTATGCAGCTTCCATAAAATTCACAAACATTTGGATTTCTGGGCTTTGCCA;CE=1.89393;CONSBP=72;RDRATIO=1.36851;SOMATIC GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-13.6735,0,-72.9675:137:PASS:2159:6402:2799:3:0:0:27:8 0/0:0,-7.81718,-79.9904:78:PASS:2431:4897:2759:2:0:0:26:0 ./.:.:.:.:.:.:.:.:.:.:.:. ./.:.:.:.:.:.:.:.:.:.:.:.
Could you elaborate why this behaviour is occurring and how to mitigate the same? Thanks again!
I am currently attempting to
merge/collapse
VCFs produced by DELLY, LUMPY and MANTA using Truvari. Two of the VCFs produced are in the 4.2 specification and one is produced in the 4.1 specification. I wanted to inquire whether Truvari can handle VCF files with different format versions, and if so, how does it handle this?