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Pre_processing BAM file for variant calling using RNA-seq data

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?

wheat_rna-seq rna-seq alignment
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written by ammarsabir15 ammarsabir15

1 answer

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.

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written by WouterDeCoster WouterDeCoster

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

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written by ammarsabir15 ammarsabir15

Also I want to ask why it is a problem?

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written by ammarsabir15 ammarsabir15

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

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written by ammarsabir15 ammarsabir15

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

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written by Ram Ram

lol ... well, you can do it but just be very aware of the limitations.

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written by Kevin Blighe Kevin Blighe

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