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PhaseByTransmission

BerntPoppBerntPopp Member
edited October 2012 in Ask the GATK team

Hello,

while using PhaseByTransmission I always get this error:

INFO 23:07:16,945 PhaseByTransmission - Caution: Family F1 has 1 members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.

This is the PED file:

F1 26779 31599 31600 2 2

F2 31599 0 0 2 0

F3 31600 0 0 1 0

And the command line:

java -Xmx2g -jar /home/common/GenomeAnalysisTK-2.1-13/GenomeAnalysisTK.jar \
-R /home/common/hg19/ucschg19/ucsc.hg19.fasta \
-T PhaseByTransmission \
-V 38Ind_batch01_ped_snps.raw.SNP.filtered.vcf \
-ped familys.ped \
-pedValidationType SILENT \
-o 38Ind_batch01_ped_snps.raw.SNP.filtered.phasedBT.vcf

PhaseByTransmission then only rewrites the VCF file without any phasing done.
Is there something wrong with the commandline or is the PED file malformated?

Best Answer

  • LaurentLaurent Member, Broadie
    Accepted Answer

    Dear Bernt,

    The first column of the ped file is the family ID and hence should be the same for all members of a family. In your current ped file, you declare 3 distinct families (F1, F2, F3). The rest of your ped file is correct, simply changing the family ID so that all your family members are in the same family will do.

    Cheers,
    Laurent

Answers

  • LaurentLaurent Member, Broadie
    Accepted Answer

    Dear Bernt,

    The first column of the ped file is the family ID and hence should be the same for all members of a family. In your current ped file, you declare 3 distinct families (F1, F2, F3). The rest of your ped file is correct, simply changing the family ID so that all your family members are in the same family will do.

    Cheers,
    Laurent

  • Dear Laurent,

    thank you very much it worked!

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