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Old 09-27-2012, 06:15 AM   #1
krueml
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Location: US

Join Date: Aug 2012
Posts: 3
Default variant calling with SAMtools

Hi, I am trying to repeat a papers steps to detect somatic variants. My earlier steps were using bwa, picard sortsam and addedreadgroup, and gatk indelrealigner. now I'm stucking at the variant calling step where the paper says I should use SAMtools varfilters with 3 different options. I found out how to put 2 of them but the 3rd one gives me headache since last week:

Minimum consensus quality set to 20

My pipeline looks like this for now:
samtools mpileup -M 255 -ugf ref.fasta realigned.bam | bcftools view - | vcfutils.pl varFilter -Q 43 | awk '$6>=50'> var.flt.vcf


I also found out on http://samtools.sourceforge.net/cns0.shtml that there should be a column called consensus quality or phred scaled likelihood that genotype is wrong, respectively, but I cannot find that column in my data.
After
samtools mpileup -M 255 -f ref.fasta realigned.bam > raw.pileup
my data looks like this. And there arent so many columns (even with option -OABs with does not change):


1 569924 T 2 .. GI
1 569925 G 2 .. HI
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Thank you!

K
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