Filtering Bam files with bam-filter

This executable is useful to filter Aligned PacBio bam file’s according to the values of some columns. It offers the following options:

<BAM-FILE>

Input file in BAM format. The output will be another BAM-FILE with the same name but prefixed with ‘parsed.’.

For example:

$ bam-filter mydata.bam ...

will produce, as output a file named parsed.mydata.bam.

-l <INT>, --min-dna-seq-length <INT>

Minimum length of DNA sequence to be kept (default: 0, ie. do not filter).

-r <INT>, --min-subreads-per-molecule <INT>

Minimum number of subreads per molecule to keep it (default: 1).

-q <INT>, --quality-threshold <INT>

Quality threshold of the sample. Between 0 (the lowest) and 255 (the highest) (default: 0).

-m <MAPPING>[ <MAPPING> ...], --mappings <MAPPING>[ <MAPPING> ...]

Keep only the requested (space separated) list of mappings (default: keep all).

-R <NUM>, --min-relative-mapping-ratio <NUM>

Minimum ratio (wanted mappings/all mappings) to keep the subread (by default all the subreads are taken).