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a newbie question about understanding the phased data

gatknewbie_mssmgatknewbie_mssm new york, Member

Not a techie person but an end user/reader of VCF. I came across the following data but could not comprehend why genotype 6 is suddenly unphased. Any help?? Thanks a lot.

ps. NOT sure if this is an appropriate question for GATK forum? Please help remove it if it isn't. I do believe phasebytransmission was run - (and can find out more info about other tech details if/when asked)

 #CHROM POS ID  REF ALT FILTER  INFO    FORMAT  child   father  mother
1#chr11 118957735   .   G   T   PASS    .   GT:AD:DP:GQ:PL:TP   0|0 0|1 0|0
2#chr11 118957930   .   T   TAA,TA  PASS    .   GT:AD:DP:GQ:PL  0/0 0/0 0/0
3#chr11 118957947   .   AAAG    A   PASS    .   GT:AD:DP:GQ:PL:TP   0|0 0|0 0|0
4#chr11 118957948   .   AAG A   PASS    .   GT:AD:DP:GQ:PL:TP   1|0 0|0 1|1
5#chr11 118957949   .   AG  A   PASS    .   GT:AD:DP:GQ:PL:TP   1|1 1|0 1|0
6#chr11 118957950   .   G   A   PASS    .   GT:AD:DP:GQ:PL:TP   0/0 0/0 0/0


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Phasing three hom-ref sites would not be meaningful. I see you have one such site that is phased but that might be an artifact of whatever tool produced this. If you think about what that represents you can see that it's uninformative.

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