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Old 04-12-2013, 12:18 PM   #3
huma Asif
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Location: Japan

Join Date: Oct 2010
Posts: 53
Unhappy VCF file from lifescope

hi everyone
i need help in understanding the VCF file output
GT: GQ : DP: FDP: AD: AST: AMQV
0/1: 13: 22: 13: 2,9: 2,6: 31,21
CHROM POS ID REF ALT QUAL FILTER INFO
chr1 762273 . G A . PASS DP=22
Result:
At this site GT is 0/1 (i guess it is heterozygous) the confidence is not good GQ=13 largely because there are only 22 reads at this site DP= 22, why AD is 2,9 what i understand is it should be equal to DP
i read somewhere that this Sum can be smaller than DP because low-quality bases are not counted is it correct.
how will this FDP, AST and AMQV be interpreted?
Another question is
how i can correlate the SNPse to specific diseases by comparing allelic frequencies
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