bamreorder

Format

cg bamreorder bamfile resultbamfile referencegenome

Summary

Changes the order of the contigs/chromosomes in a bam file

Description

This command changes 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 without a match, or with matching names but different size are dropped from the bam.

Arguments

bamfile: bamfile
resultbamfile: name of resulting reordered bamfile
referencegenome: a indexed fasta file of the genome. If the file is not indexed, the command will try to create the index (using samtools)

Options

-threads numthreads: number of threads to be used (for compressing the final bam file)

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