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Old 03-02-2011, 01:36 PM   #1
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Location: Canada

Join Date: Mar 2011
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Default samtools mpileup for SNP genotyping (VCF4)

Hi all,
I have six samples (s1-s6), the breakdown of the SNP (ref/alt) at contig1 position 3929 is as follows:-

s1, 3, 0
s2, 0, 16
s3, 24, 0
s4, 1, 16
s5, 14, 0
s6, 8, 14

Most (if not all) called bases have reasonable quality scores.

I am trying to understand the output generated by samtools mpileup ( 0.1.12-10 (r896), default parameters) below

contig1 3929 . G T 6.9 . DP=96;AF1=0.2036;
Some strange observations :
a) the QUAL column=6.9, which indicates Phred-scaled probability of all samples being homozygous reference, seems unreasonably low, given the number of reads that support "ALT";
b) one would think GQ (genotype quality) for s2 should be a lot higher,given that there is zero count from REF;
c) shouldn't 0/1 (instead of 0/0) make more sense for s6.

Did I miss something here? Appreciate any help I can get.
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