Varscan2: run in parallel / merge mpile output from diff run into single mpileup

Question

[Chirag Nepal]

Hi all,

I am using varscan2 to identify SNPs in our data (exome study comparing normal/tumor from 5 patients).

For testing I used only two pairs,

samtools mpileup -f assembly.fa ST1_normal.bam ST1_tumor.bam ST2_normal.bam ST2_tumor.bam > myTestData.mpileup

It takes long time, is there a way how can I run in parrallel. Or if I run it in single pair (tumor/normal), can I simply concatenate all mpileup files into single output file, which I can input to varscan2 for SNP calling.

Thanks for your help !

Cheers
Chirag

Answer 1

[Pierre Lindenbaum]

Run one mpileup in parallel for each chromosome, region, using the option -l or -r

-l FILE     BED or position list file containing a list of regions or sites where pileup or BCF should be generated
-r STR  Only generate pileup in region STR

samtools mpileup -f assembly.fa  -r chr1 (...) >  myTestData1.mpileup
samtools mpileup -f assembly.fa  -r chr2 (...) >  myTestData2.mpileup
samtools mpileup -f assembly.fa  -r chr3 (...) >  myTestData2.mpileup
(...)

[Chirag Nepal]

Dear Pierre,

Thanks for the answer. So just to be clear i need to run separately for each chromosome

samtools mpileup -f assembly.fa  -r chr1 Nor_1.bam Tum_1.bam Nor_2.bam Tum_2.bam Nor_3.bam Tum_3.bam Nor_N.bam Tum_N.bam > mplie_N1.mpileup
samtools mpileup -f assembly.fa  -r chr2 Nor_1.bam Tum_1.bam Nor_2.bam Tum_2.bam Nor_3.bam Tum_3.bam Nor_N.bam Tum_N.bam > mplie_N2.mpileup

So to make these run in parallel, i need to submit the jobs separately in different bash scripts ? I guess if I put all these commands in a single bash script they will run sequentially. Right ? Though it might be faster when chr is separated.

Next, when we have this multiple mpileup results, can we simple concatenate in single file :

like cat mplie_N1.mpileup mplie_N2.mpileup > mplie_total.mpileup

Or does samtools have some functions to concat them.

thanks !

Cheers
Chirag

[Pierre Lindenbaum]

So to make these run in parallel, I need to submit the jobs separately in different bash scripts?

Use GNU parallel or GNU make with option -j How To Run Muscle In Batch?