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).