How to call somatic mutations from vcf files
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
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Pierre Lindenbaum
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DS •
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samtools mpileup is deprecated for calling VCF. use bcftools mpileup. https://samtools.github.io/bcftools/howtos/variant-calling.html
call all your samples in the same cmd.
bcftools mpileup -f reference.fa s1.bam s2.bam s3.bam s4.bamI got this error when running
bcftools mpileupyour version of bcftools is just too old.
Don't delete questions please.