In exome sequencing, specific interval list (-L) is used by each company to capture particular region. But all exome in the genome will be in particular regions (the default region of exomes mentioned here.
$ 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
So what is the difference between using custom interval list (-L option used in GATK best Practice and default interval list. How the accuracy of the output is affected?
The question got answered here [https://gatkforums.broadinstitute.org/gatk/discussion/10480/what-are-the-differences-in-using-default-and-custom-interval-list-l-for-exome-seq]
There area couple of answers on the linked thread but speaking from experience, I would always use the interval file that was used by the company to create the library.
When you perform your alignments, if you include regions that were not used in the design of the library, i.e. if you use someone elses interval file that includes regions that your capture wasn't designed to capture but did so anyway, then you are including an unknown in your downstream work. You might have captured that region by accident, and this won't be reproducible across your samples. So if you end up looking for copy number variable regions, this region may show up, as it didn't capture efficiently across your samples.
This is just one example of how using regions not defined in your particular library might affect your work. In a practical sense you have to consider these factors.
@Sophie
I have asked the same question in the GATK forum and they have replied in following way
"Eventually it all comes down to what you are looking for in practice. I have seen bed files provided by manufacturers not representing all captured regions properly in the past. Yet I have seen manufacturers not being able to provide proper uplifted regions for exome capture kits for hg38 as well. Majority of the kits are still being produced for hg19 but for hg38 uplifting that bed file results in loss of regions also. I am not afraid of capturing more false positives than loosing true positives due to CNVs not covered by bed files.
This is totally my belief BTW"
Written By SkyWarrior
https://gatkforums.broadinstitute.org/gatk/discussion/comment/43261
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