v1.7.0
BamM v1.7.0 now depends on Samtools 1.0 or greater (recommended Samtools 1.3 at least).
New features (as of v1.6.0) include:
bamm make
flag -u
or --keep-unmapped
will keep unmapped reads in BAM output.
bamm filter
flag -v
will keep only reads which do not meet specified mapping stringency.
An example application of these features would be using BamM to filter contamined reads, by mapping to a reference using bamm make -u
and then running bamm filter -v
and extracting the reads (e.g. with samtools fasta
).