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Variant calling on RNA seq using GATK pipeline

I was trying to do variant calling on RNAseq data using GATK pipeline.

but when i used

./gatk HaplotypeCaller -R genome.fa -I Aligned.sortedByCoord.out_dedup.bam -O output.vcf

Output.vcf file is not created. So can any one please help me...

rna-seq
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updated by lakhujanivijay lakhujanivijay • written by renu18july • renu18july

Hello renu18july,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

Additionally, do you see any error message? If yes, please post it here.

• 1 views • link
written by lakhujanivijay lakhujanivijay

Thanks a lot . No error msg but output file is not created....

• 1 views • link
written by renu18july • renu18july

Paste the output. Also, please be sure that you are aware of the limitations of calling variants from RNA-seq data. You will miss a large chunk of genomic variants by analysing data in this way.

• 1 views • link
written by Kevin Blighe Kevin Blighe

1 answer

Please be aware of the limitations of calling variants from RNA-seq data: A: Inferring genotype based on RNA sequnces

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written by Kevin Blighe Kevin Blighe

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