freebayes for variant calling too slow

Question

[evafinegan]

Hi All,

I am using freebayes to call variants mainly SNPs from 200 samples. I have created bam files by aligning RNA-seq fastq files to the transcriptome. I want to make a vcf file with SNPs from all the samples. However, it seems to run fairly slow and job is not complete after three days. I am not sure if there is something wrong or is it normal speed? Thank you

freebayes  -f  transcriptome.fasta bam1 bam2-------bam200 > result_file.vcf

Answer 1

[JC]

Freebayes is running in a single core, in general, you can split the task per chromosome, check the parallel script https://github.com/ekg/freebayes/blob/master/scripts/freebayes-parallel

[evafinegan]

Is it a python script? Is there a way to split the regions in linux and use multi-threading. Thank you!

[JC]

That is pure BASH using GNU parallel

[evafinegan]

I meant the script to generate chunks of regions.

[JC]

it doesn't need multithread, it simply reads the Fasta and define chunks https://github.com/ekg/freebayes/blob/master/scripts/fasta_generate_regions.py

[evafinegan]

Got it, thanks!