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GATK Input as list of BAMs

roger_droger_d Redwood CityMember

The GATK documentation states the -I arguement can be List[String], which when using HaplotypeCaller or UnifiedGenotyper would produce a multisample vcf.

However, I am confused as to how exactly I present my list of bam files. Is there a way to pass in t
he name of a text file which contains a list of many bam files, something like
path/to/bam_1.bam
path/to/bam_2.bam
:
path/to/bam_n.bam

Answers

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