I have been trying to call variants using
bcftools call after installing it as instructed here.
The problem is that I am not getting any calls in the output vcf (it contains only the header).
My bam files were aligned with
bwa-mem and processed with GATK pipeline. They have worked well with muTect and VarScan.
I have tried many parameter combinations e.g.
-DgB , for mpileup and
-mv for bcftools, in vain.
The versions I am using are samtools 0.2.0-rc7-54-ge35361b and bcftools 0.2.0-rc7-13-gca1a8b5
Does anyone know what the problem might be?
An example commandline I used is below:
samtools mpileup -u -f ref.fa -b sampleList | bcftools call -cv - > output.vcf