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Interval list for GATK tool Haplotype Caller

Hello, I am currently using GATK's tool haplotypecaller to do variant discovery for some RNA-seq data. The is a very long running process so I have been looking at how to ways to optimize speed. It is mentioned that you can pass an interval list to HaplotypeCaller to speed up performance. It mentions that you can pass a vcf as the interval list to use. I am wondering if it is appropriate to use a reference vcf such as Ensembl's GRCH38.vcf file, as this will be intervals for genes and my variant discovery will only be looking within genes since that is the nature of the RNA-seq data.

Does make sense to use? I cant find much in the docs about what kind of interval list to use for RNA-seq data, it is mostly about whole genome or targeted exome. If that vcf is not proper to use, what interval list or how do I create an interval list to be used by HaplotypeCaller to speed up processing for this RNAseq data

rna-seq snp
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written by jeremy • jeremy

Yes, you can specify a interval list, just use the -L option and point to a BED file containing your intervals!

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written by brunobsouzaa brunobsouzaa

2 answers

As I know, intervals in HaplotypeCaller are BED files (Genomic positions). You specify the regions where to call variants.

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written by abedkurdi10 • abedkurdi10

However, my question is for RNAseq, are the intervals just going to be every gene, so for example a BED file of the entire transcriptome?

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written by jeremy • jeremy

Yes, for every gene or for genes of interest

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written by abedkurdi10 • abedkurdi10

However, my question is for RNAseq, are the intervals just going to be every gene, so for example a BED file of the entire transcriptome?

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written by jeremy • jeremy

Hi jeremy,

This reply is better suited as a comment on abedkurdi10's answer. Could you make the appropriate change please? That would involve the following steps:

  1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
  2. Click on Add Comment on abedkurdi10's post here: A: Interval list for GATK tool Haplotype Caller
  3. Paste the copied text
  4. Click on the green Add Comment button
  5. Click on moderate back in your answer here: A: Interval list for GATK tool Haplotype Caller
  6. Choose Delete Post
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Thank you!

P.S: Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate.

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written by Ram Ram

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