Samtools mpileup multi thread?

[bioinfun]

Hi

I am using mpileup on 296 sequenced genomes. Obviously this takes quite a long time, but I was wondering if anyone knows a way of making it faster, like using multi thread. This is my command:

samtools mpileup -ugf ref.fas *.bam | /usr/local/samtools/bcftools/bcftools view -vcg - > my.vcf

Thanks

[maubp]

Have you considered dividing the task up by chromosome/reference, and running each in parallel?

[bioinfun]

No I haven't. Can you expand further please.

[maubp]

The simplest way to do this is to divide the work up by reference sequence. This will be most effective on a cluster, so as to spread the IO load. i.e. If your organism has 20 chromosomes, submit 20 jobs to your cluster, each doing 'samtools mpileup' on a different chromosome.

[rnaseek]

Splitting by chromosomes is the way to go. You might also want to watch for hard disk storage used at each step(chr), as each mpileup file can just blow up. Even better to parse each mpileup file and store it in a smaller file if you dont need to keep everything in mpileup file.