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  • genotype likelihood inconsist with genotype field in mpileup output

    hi, all
    I call SNPs using mpileup from samtools, I got strange results like:

    Gm01 2923425 . A G,C 999 . DP=308;VDB=0.0224;AF1=0.6;G3=0.4,1.742e-06,0.6;HWE=0.00948;AC1=8;DP4=46,45,111,93;MQ=55;FQ=999;PV4=0.61,1,4.6e-0
    9,1 GT:PLP:SP:GQ 1/1:255,157,0,255,157,255:52:0:99 0/1:255,255,255,169,169,0:56:0:3 0/0:200,255,255,0,255,255:59:2:48 1/1:255,102,0,255,102,25
    5:34:0:99 0/0:0,154,255,154,255,255:51:0:99 0/1:255,255,255,90,90,0:30:0:3 1/1:255,39,0,255,39,255:13:0:37

    According VCF format specification:
    1000genomes.org is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, 1000genomes.org has it all. We hope you find what you are searching for!


    the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc.

    However, in my case, for example,
    GT:PLP:SP:GQ 0/1:255,255,255,169,169,0:56:0:3
    the six field from PL string has the lowest value-"0", thus the genotype might be CC, so the GT field should be 1/1, but I get 0/1 in this case.

    another example:
    0/0:200,255,255,0,255,255:59:2:48
    the forth field was "0", thus genotype might be A/C, and GT field must be 0/1, I get 0/0 in this case.

    I am confused about this.

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