We sequenced the exoms of about 50 genes.
UnifiedGenotyper seems to call variants along the whole genome.
How can I restrict the region of variant calling?
Yes, your list format will work.
Have a look at this documentation that explains more about how input files are used with -L: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_engine_CommandLineGATK.php#--intervals
You can use the -L argument. Please read about it here: http://gatkforums.broadinstitute.org/discussion/4133/when-should-i-use-l-to-pass-in-a-list-of-intervals#latest
Thank you for your explation.
Could you provide a sample table?
I format the intervals accoding to it.
Would a list file with one column: chr20:1-100
After reading the link, I guess a bed file should also work.
Hi, I am wondering in which parts of GATK best practice can use -L option?
You can use the -L option with any tool in GATK.
Here is a link to all arguments you can use with all tools in GATK. You will find -L to be one. https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_engine_CommandLineGATK.php