How to call somatic mutations from vcf files

Question

[DS]

I have created two vcf.gz file with samtools mpileup and bcftools index, and then i compare them with bacftools isec

it outputs 4 .vcf files. But how can i filter out somatic mutations from these files?

Thanks

[Pierre Lindenbaum]

samtools mpileup is deprecated for calling VCF. use bcftools mpileup. https://samtools.github.io/bcftools/howtos/variant-calling.html

[Pierre Lindenbaum]

it outputs 4 .vcf files.

call all your samples in the same cmd. bcftools mpileup -f reference.fa s1.bam s2.bam s3.bam s4.bam

[DS]

I got this error when running bcftools mpileup

[E::main] unrecognized command 'mpileup'

[Pierre Lindenbaum]

your version of bcftools is just too old.

Don't delete questions please.