Option "calmd"; Reporting indels and Somatic mutations for Whole Exome Seq data:
Hello,
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.
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.