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  • VCF question concerning PL and GQ scores in Sanger Mouse Genomes data

    Hi all,

    I have just started to try to work with VCF files, and have read through the specifications here (https://github.com/samtools/hts-specs) and also on the 1000 genomes website. However, I am still a bit confused about the difference between Genotype Quality (GQ) and Genotype Likelihoods (PL) in the SAMPLE columns. Specifically, I am using the mgp.v3.snps.rsIDdbSNPv137.vcf file downloaded from Sanger Mouse Genomes (ftp-mouse.sanger.ac.uk/current_snps/mgp.v3.snps.rsIDdbSNPv137.vcf.gz), and am confused by the following line:

    Code:
    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  129P2   129S1   129S5   AJ      AKRJ    BALBcJ  C3HHeJ  C57BL6NJ        CASTEiJ ....etc
    1       185273864       .       T       G,A     208.22  StrandBias      AC1=1;AC=12,2;AF1=0.5336;AN=36;DP4=251,455,132,218;DP=1083;MDV=99;MQ=31;MSD=27;PV0=0.054;PV1=1;PV2=1;PV3=1;PV4=0.054,1,1,1;QD=0.8148;SB=0.8512;VDB=0.0308       GT:GQ:DP:SP:PL:FI    1/1:99:27:13:198,0,9,.,.,.:1    1/1:99:91:40:255,0,57,.,.,.:0   1/1:99:19:19:129,0,56,.,.,.:1   0/0:.:43:3:0,.,.,.,.,.:1        1/1:99:53:44:255,0,163,.,.,.:0  0/0:.:69:17:0,.,.,.,.,.:1       0/0:.:61:7:0,.,.,.,.,.:1    0/0:.:61:0:0,.,.,.,.,.:1 1/1:99:59:38:255,0,107,.,.,.:1 ......etc
    It is the field for CASTEiJ that confuses me:

    FORMAT = GT:GQ: DP:SP:PL:FI
    CASTEiJ = 1/1:99:59:38:255,0,107,.,.,.:1

    GT indicates the genotype is Alt1/Alt1, and the GQ field suggests this is very unlikely to be wrong. However, the PL field (255,0,107,.,.,.) suggests that the 0/1 (Alt/Ref; i.e. heterozygous) genotype is most likely.

    So - I do not understand this apparent discrepancy between the GT and PL fields?

    More generally, I do not completely understand what the difference is between a Genotype Quality (GQ), and the Genotype Likelihoods (PL). If anyone is able to explain these to me in simple (not too statistical!) terms I would be incredibly grateful!

    Ultimately, I would like to apply a simple filter to extract all CASTEiJ SNPs that are "high quality" (very unlikely to be wrong). I thought a good way to do this would be to take all entries with the CASTEiJ field like this: 1/1:xx:xx:xx:xx:1 (i.e. Alt/Alt, that passes filter), with either a "good" GQ score, or a "good" PL score for the Alt/Alt. Does this sound sensible?

    Many thanks, Alex

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