Is it possible to use CRISP to working with low coverage WGS data?

vibansal / crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples

MIT License

19 stars 8 forks source link

Is it possible to use CRISP to working with low coverage WGS data? #31

Closed raksasa closed 1 year ago

raksasa commented 1 year ago

Hi, I'm trying to call indel from many low coverage WGS data from many individuals. I guess I can improve indel calling sensitivity if I treat them as pool-seq. Is it fine to use CRISP to work with such data? If yes, how should I specify parameter '--bam'? I guessed --bam received a bam file contains pooled reads, so I should merge all my individual bams into one bam?

vibansal commented 1 year ago

I don't think that merging bams will give good results. I would suggest running CRISP using pool size 2 and "--EM 0" option.