Test-drive the GATK tools and Best Practices pipelines on Terra
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a newbie question about understanding the phased data
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