ekg/freebayes — Issue #27: Seemingly clear Var/Var SNP reported as unlikely Ref/Var
Author: jorgsk
Created: 2012-01-06 10:21:01+00:00
State: open

I have a SNP that seems to be a clear G -> A substitution in two different cell lines. Indeed, mpileup reports it as

GT:PL:GQ	1/1:102,5,0:16	1/1:140,55,0:65

However, freebayes reports it as

GT:GQ:DP:RO:QR:AO:QA:GL

Cell Line 1
0/1:73.6778:19:3:105:16:507:-45.9469,-2.73325,-9.8

Cell Line 2
0/1:72.1561:50:5:170:45:1427:-128.747,-8.72542,-15.64

So it reports this to be an AB variant and even a very unlikely one.

I'm using version 0.9.4 pulled from Git yesterday, last commit was 094879e3e7.

The command I run is:

freebayes -f hg19.fa -v variants.vcf GM12878_sorted_proper.bam K562_sorted_proper.bam

Links to the bam-files in question:

http://www.nt.ntnu.no/users/jorgsk/GM12878_sorted_proper.bam
http://www.nt.ntnu.no/users/jorgsk/K562_sorted_proper.bam

The hg19 has the chromosomes from 1 to M, not the random ones.