Advice for indel calling

Question

[jparker4]

Hi, I am doing some indel calling on some RNA-seq data. I wondered if there was a preferred indel caller, and are there any pre-processing steps necessary in an indel calling pipeline, or does it depend on the caller used. Thanks.

[grant.hovhannisyan]

You can try using the best practises of GATK with RNAseq data https://gatkforums.broadinstitute.org/gatk/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full-detail