Pre_processing BAM file for variant calling using RNA-seq data

Question

[ammarsabir15]

I want to call variants using whole genome RNA-seq datasets of wheat. I have generated BAM files using STAR, I want to ask should I apply any post processing steps to these BAM files like Removing duplicates, removing reads based on quality scores etc before performing further downstream analysis?

Answer 1

[WouterDeCoster]

Not the answer you are looking for, but while it's technically possible RNA-seq is absolutely not a suitable technology for variant calling purposes. I can imagine in a hexaploid wheat (I believe?) this is even more of a problem.

[ammarsabir15]

Yes it is hexaploid and I have to call variants on it sadly!!!

[ammarsabir15]

Also I want to ask why it is a problem?

[Kevin Blighe]

Dear ammarsabir15, in order to begin to understand the limitations with this, please take a look at my answer here: A: Inferring genotype based on RNA sequnces

[ammarsabir15]

@Kevin Blighe thanks for your comments, also can you give answer to the question I asked above?

[Ram]

He did. His answer was "Don't do what you're trying to do"