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PhaseByTransmission: passing a parent/child pair on a multiple vcf

palmeirapalmeira LiegeMember ✭✭

Dear GATK,

I am trying to run PhaseByTransmission on a parent/child pair on a multiple vcf.gz (with --pedigreeValidationType SILENT) but, although not getting any errors, the output is quite strange and indicates that the pedigree has not been taken into account properly. Does anyone know how to pass a parent/child pair to this tool?

Here is some info on my data:

$ cat tmp_1.ped
Fam1 P20__ 0 0 2 0 Fam1 P10__ 0 P20__ 1 0

$ grep CHROM $vcf
#CHROM POS ID REF ALT QUAL FILTER INFOFORMAT C1B__ C2B__ C3B__ C4B__ C5B__ C6B__ C7B__ P10__ P14__ P20__ P24__P4__ P5__ P7__

INFO 10:42:44,130 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 10:42:45,414 PhaseByTransmission - Number of complete trio-genotypes: 0 INFO 10:42:45,415 PhaseByTransmission - Number of trio-genotypes containing no call(s): 0 INFO 10:42:45,415 PhaseByTransmission - Number of trio-genotypes phased: 0 INFO 10:42:45,415 PhaseByTransmission - Number of resulting Het/Het/Het trios: 0 INFO 10:42:45,415 PhaseByTransmission - Number of remaining single mendelian violations in trios: 0 INFO 10:42:45,416 PhaseByTransmission - Number of remaining double mendelian violations in trios: 0 INFO 10:42:45,416 PhaseByTransmission - Number of complete pair-genotypes: 0 INFO 10:42:45,416 PhaseByTransmission - Number of pair-genotypes containing no call(s): 0 INFO 10:42:45,416 PhaseByTransmission - Number of pair-genotypes phased: 0 INFO 10:42:45,417 PhaseByTransmission - Number of resulting Het/Het pairs: 0 INFO 10:42:45,417 PhaseByTransmission - Number of remaining mendelian violations in pairs: 0 INFO 10:42:45,417 PhaseByTransmission - Number of genotypes updated: 0 INFO 10:42:45,446 ProgressMeter - done 0.0 1.0 s 15.2 d 100.0% 1.0 s 0.0 s INFO 10:42:45,446 ProgressMeter - Total runtime 1.32 secs, 0.02 min, 0.00 hours

Answers

  • LaurentLaurent Member, Broadie ✭✭

    Hi Palmeira,

    Looking at your ped file it seems (although I might be wrong) that it is space delimited. I'm not 100% sure but think it should be tab delimited. Could you also please provide the command line you're running?

    Thanks,
    Laurent

  • palmeirapalmeira LiegeMember ✭✭

    It is indeed space delimited, I have just tried the same file with tabs instead of spaces and nothing changes.
    Here is my command line:

    $GATK -T PhaseByTransmission -R $ref -V $vcf -ped $tmpped --pedigreeValidationType SILENT -o $vcfout -et NO_ET -K $noET

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