I am using samtools for variant calling. The issue I am having is that samtools mpileup seems to be taking a very long time. I am running samtools on a cluster and have a set how long samtool will run. The first time I tried this I gave it 7 days to run with 256 Gbs of RAM. The resulting file only had two chromosome of variant calling. I am working with about 40 samples and they range from 10-30 Gbs so I realize it will take some time. I am just worried I am doing something wrong here? I feel like it shouldn't take this long.
Here is the command I am using for samtool
samtools mpileup --redo-BAQ --min-BQ 30 --per-sample-mF -C 50 --output-tags DP,DV,DPR,INFO/DPR,DP4,SP -u -f refgenome.fa sample1.bam sample40.bam > allsample.bcf
What do you think? Any suggestion on how to speed this up? I am using -C 50 because I used bwa.