Is there any way to generate interval list from available exome data?

Question

[Karma]

Hi all, I am following the "best practice" suggested by broad institute to call variants from whole exome sequencing data. Currently, I am using Mutect2 to call variants from tumor sample and normal sample based on latest reference genome GRCh38. But, I don't have interval list to use -L option. Is there any way to generate interval list from exome sample which I have? or Is there any default interval list for exome data? Thank You

[ivivek_ngs]

you should have an interval list which you can generate as Pierre suggested, however, if you are using Agilent kit when the v4/v5 that were used for the library enrichment for getting the exonic baits should have an internal bed file. This should be provided by the company or should be available online. You have to know which kit you have used and then you can ask the wet lab person if they have the corresponding bed file for it or you can search online. Those baits should serve as intervals for your exon enrichment. It is just a way to understand the baits which used have proper sequencing coverage or not then your precision on variants calls around those baits(intervals) should be better. Hope this is clear!

[Pierre Lindenbaum]

Hello Phoenix!

It appears that your post has been cross-posted to another site: https://gatkforums.broadinstitute.org/gatk/discussion/10357/

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Pierre Lindenbaum]

Is there any default interval list for exome data?

something like:

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz" |\
    gunzip -c | cut -f 3,5,6 | sort -t $'\t' -k1,1 -k2,2n | bedtools merge -i - > exome.bed

[Karma]

Hi, Pierre Lindenbaum

What will be the accuracy of variant calling when we are using default interval list?

Thank You