gatk4中的interval是什么？？

Posted 2022-12-08 qq_21478261

以gatk Mutect2为例

--intervals,-L <String>       One or more genomic intervals over which to operate  This argument may be specified 0 or more times. Default value: null. 

-L exome_autoXYM.intervals 

intervals到底是啥？是bed？是Picard.interval_list？是VCF files？

本文详细搞定这个问题。

Interval lists define subsets of genomic regions, sometimes even just individual positions in the genome. You can provide GATK tools with intervals or lists of intervals when you want to restrict them to operating on a subset of genomic regions. There are four main types of reasons for doing so:

• You want to run a quick test on a subset of data (often used in troubleshooting)
• You want to parallelize execution of an analysis across genomic regions
• You need to e