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Old 01-10-2012, 03:32 PM   #1
Location: US

Join Date: Oct 2011
Posts: 47
Unhappy Option "calmd"; Reporting indels and Somatic mutations for Whole Exome Seq data:


Q1) I read that one should use "calmd" option before running these two commands. So I did following. The last two commands below gave me empty vcf files when I use .baq.bam as input. What am I doing wrong?

> samtools calmd -Abr foo.sorted.bam human_19.fa > foo.baq.bam
> samtools index foo.baq.bam foo.bam.bai
> samtools mpileup -u hg19.fa foo.sorted.baq.bam | bcftools view - > foo.sorted.calmd.bcf
> bcftools view foo.sorted.calmd.bcf | vcfutils varFilter -D200 > foo.d200.flt.calmd.vcf

Q2) How do I call and report somatic mutations after getting the vcf files as above?

Many thanks.

Last edited by angerusso; 01-10-2012 at 05:02 PM.
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