Closed:RNA-Seq Variant Calling

Question

[user5212]

I have RNA-seq data from two separate projects:

== Project 1==

• We received an RNA sample for a particular antibody strain. Over 150M, PE150 reads were generated.

== Project 2 ==

• We prepared another library from the same RNA sample. Over 24M, PE300 reads were generated.

I used the The GATK Best Practices for variant calling on RNAseq pipeline to analyze both projects. In Project 1, the VCF file reported no variants. In Project 2, the VCF file reported 4 variants.

What's an explanation for the difference in the VCF reports when the same GATK pipeline was used for two libraries prepared from the same sample?

The commands I used: https://pastebin.com/zh07Dvmr. Note: I ran the pipeline using Snakemake.

Update: I posted my question to the GATK forums.