I'm trying to call SNPs from a pooled DNA sample using the PoPoolation2 pipeline. I'm stuck on a step that requires me to make a mpileup file from my BAM files. According to multiple tutorials this should work;
samtools mpileup -B input1.bam input2.bam > out.mpileup
However, when I try it makes an empty file.
I've tried adding a reference, re-sorting my BAM files and I checked for errors using Picardtool's ValidateSamFile. Even weirder, I can generate a file using GATK's Pileup command. Any ideas why
samtools mpileup doesn't work for me?