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Old 09-27-2017, 02:31 AM   #1
snijesh
Junior Member
 
Location: india

Join Date: Jan 2017
Posts: 4
Default Differences in using default and custom interval list (-L) for exome seq?

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.

Code:
$ 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?
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