Question

Variant calling on RNA seq using GATK pipeline

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6.5 years ago

renu18july • 0

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 • 2.5k views

ADD COMMENT • link updated 6.5 years ago by lakhujanivijay 5.9k • written 6.5 years ago by renu18july • 0

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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.

ADD REPLY • link 6.5 years ago by lakhujanivijay 5.9k

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

ADD REPLY • link 6.5 years ago by renu18july • 0

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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.

ADD REPLY • link 6.5 years ago by Kevin Blighe 88k

score 0 · Answer 1 · 2018-06-25

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6.5 years ago

Kevin Blighe 88k

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

ADD COMMENT • link 6.5 years ago by Kevin Blighe 88k