Merge bam files

Question

[khatami.mahshid]

I already ask a question about this, but I didn't get my answer complete.

Merge bam files and get VCF file

I have 6 bam file that one of them is just 2 Mb and one is 2 Gb. I think the comparison between VCF file of these bam files is not fair, because they don't have equal read. so I want to merge all the reads ( probably bam files) to a single file and then get the VCF file output of this. I want to do following command:

samtools merge file_1.bam file_2.bam ... -o merge.bam
samtools mpileup -f reference.fa merge.bam output.vcf

am I doing right?

[jkbonfield]

You should be using bcftools mpileup now as the samtools one is deprecated.

Also note you can specify multiple files directly with mpileup and they'll be merged in-situ as it processes them so there is no need to merge them manually. Eg:

bcftools mpileup -f reference.fa -o output.vcf file_1.bam file2.bam