GenomeComb
Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)
cg bamreorder bamfile resultbamfile referencegenome
Changes the order of the contigs/chromosomes in a bam file
This command uses picard's ReorderSam to change the order of the contigs/chromosomes in a bam file to that of the given genome reference. It first checks the contigs in each, adapting the names (e.g. 1 to chr1) where needed and checking if sizes match. Contigs with matching names, but different size are dropped from the bam.
Conversion