How does samtools mpileup work with hundreds of BAM files? I have a very large, high-coverage dataset that I need to call variants in. I suppose I could just run samtools mpileup ... *.bam, but I feel like that could turn out badly.
Alternatively, I could call variants in each BAM separately and generate many VCF files. Are there any tools out there that will merge VCF files and do the appropriate math with quality scores / read depths / etc.?
Alternatively, I could call variants in each BAM separately and generate many VCF files. Are there any tools out there that will merge VCF files and do the appropriate math with quality scores / read depths / etc.?
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