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Merge bam files

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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?

snp samtools bam vcf

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updated 6.9 years ago by zx8754

• written 6.9 years ago by khatami.mahshid •

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

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written 6.9 years ago by jkbonfield

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