About HaplotypeCaller (GATK) and using gatk4-rnaseq-germline-snps-indels workflow.

Question

[José Enrique López Obeso]

Hi guys, What is the difference between HaplotypeCaller (GATK) and using gatk4-rnaseq-germline-snps-indels workflow?, Best Regards Jose.

[DareDevil]

Your question is not clear?

HaplotypeCaller is a module within the GATK to call germline variants.

gatk4-rnaseq-germline-snps-indels is the name of the pipeline ...!!!

[Ram]

!!! lol :P

Let's keep the discussion professional - we are not in a chat room.

[José Enrique López Obeso]

Thank you very much for answering me,

so far I am clear but my question really lies in that both admit a BAM file and its output is a VCF file, but at the process level that makes them different, that is, is it the same to use both?

Best Regards Jose

[DareDevil]

generating a bam file which is aligned to the reference is common step for all the analysis. You can go through this pipeline. Spent some time on this, you will be self clarified with your doubts

[José Enrique López Obeso]

Thank you very much for answering me, I think I will do that, regards