realignIndelsGATK: Realign indels via GATK

Description Usage Arguments Details Value Author(s)

View source: R/gatk.R

Description

Realing indels using the GATK tools RealignerTargetCreator and IndelRealigner. Requires a GATK compatible genome with a name matching the alignment genome to be installed in 'path.gatk_genome'

Usage

1

Arguments

bam.file

Path to bam.file

Details

Since GATKs IndelRealigner is not parallelized, we run it in parallel per chromosome.

Value

Path to realigned bam file

Author(s)

Jens Reeder


HTSeqGenie documentation built on Nov. 2, 2018, 6:01 p.m.