Tag: MuTect

Bowtie2 hg19 reference for gatk MuTect

Bowtie2 hg19 reference for gatk MuTect 3 Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and…

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