I made snp calls on a set of 14 samples with samtools mpileup.
How do I determine the genotype call in a particular sample from the vcf file?
An example entry (some fields omitted for clarity) is:
chr10 4770821 G T,C,A 999 1/1:84,15,0,84,15,84,78,1,78,75:6:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:57,15,0,57,15,57,57,15,57,57:5:26 1/1:79,15,0,79,15,79,79,15,79,79:5:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:90,15,0,90,15,90,90,15,90,90:5:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:62,47,41,28,0,13,62,47,28,62:7:17 1/1:65,16,7,55,0,52,65,16,55,65:4:20 1/1:84,15,0,84,15,84,84,15,84,84:5:26
(GT: PL: DP: GQ)
I thought a GT field of 1/1 would mean the TT genotype, but all of the sample have this genotype, so I am confused as to where the other alternate snp calls are coming from? Also, what does it mean when all of the PL scores are 0?
Thanks!
How do I determine the genotype call in a particular sample from the vcf file?
An example entry (some fields omitted for clarity) is:
chr10 4770821 G T,C,A 999 1/1:84,15,0,84,15,84,78,1,78,75:6:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:57,15,0,57,15,57,57,15,57,57:5:26 1/1:79,15,0,79,15,79,79,15,79,79:5:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:90,15,0,90,15,90,90,15,90,90:5:26 1/1:0,0,0,0,0,0,0,0,0,0:0:11 1/1:62,47,41,28,0,13,62,47,28,62:7:17 1/1:65,16,7,55,0,52,65,16,55,65:4:20 1/1:84,15,0,84,15,84,84,15,84,84:5:26
(GT: PL: DP: GQ)
I thought a GT field of 1/1 would mean the TT genotype, but all of the sample have this genotype, so I am confused as to where the other alternate snp calls are coming from? Also, what does it mean when all of the PL scores are 0?
Thanks!
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