Bam2reg
Format
cg bam_sort ?options? ?bamfile? ?sortedbamfile?
Summary
sort a bam file.
Description
Arguments
- bamfile
- bam file to sort
- sortedbamfile
- resulting sorted bam file
Options
- -method gnusort/samtools/biobambam
- method used for sorting, must be one of
gnusort,samtools,biobambam (default samtools)
- -sort coordinate/name/hash
- what to sort on (default coordinate)
- -inputformat format
- input format (default derived drom file name extension)
- -outputformat format
- output format (default derived drom file name extension)
- -threads nrthreads
- number of threads to use
- -refseq refseq
- genomic reference sequence (needed for cram format sorting)
Category
Conversion