Variant calling on RNA seq using GATK pipeline

Question

[renu18july]

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...

[lakhujanivijay]

Hello renu18july,

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

Thank you!

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

[renu18july]

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

[Kevin Blighe]

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.

Answer 1

[Kevin Blighe]

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