Question: Is there any way to generate interval list from available exome data?
1
gravatar for Karma
17 months ago by
Karma200
India
Karma200 wrote:

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

mutect2 sequencing gatk exome • 1.6k views
ADD COMMENTlink modified 17 months ago by Pierre Lindenbaum117k • written 17 months ago by Karma200
2

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!

ADD REPLYlink modified 17 months ago • written 17 months ago by ivivek_ngs4.6k

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.

ADD REPLYlink written 17 months ago by Pierre Lindenbaum117k
3
gravatar for Pierre Lindenbaum
17 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

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
ADD COMMENTlink written 17 months ago by Pierre Lindenbaum117k

Hi, Pierre Lindenbaum

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

Thank You

ADD REPLYlink modified 17 months ago • written 17 months ago by Karma200
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