mark duplicate alignments in a coordinate sorted file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2{:bash}
fasta{:bash}
A reference genome in FASTA format
*.fasta
bam{:bash}
*.bam{:bash}
BAM file
*{.bam}
cram{:bash}
*.cram{:bash}
CRAM file
*{.cram}
sam{:bash}
*.sam{:bash}
SAM file
*{.sam}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Tools for dealing with SAM, BAM and CRAM files
