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-filter -h usage: bam-filter [-h] [-l NUM] [-r NUM] [-q NUM] [-m MAPPING [MAPPING …]] [-R NUM] [-v] [–version] BAM-FILE
Program to filter BAM files after Pacbio sequencing. Different filters can be applied on demand (by default all the filters are disabled). The order in which the filters are applied is: 1) remove rows with len of DNA sequence under some threshold; 2) take only molecules with a minimum number of subreads; 3) choose molecules with sequencing quality above some threshold; and 4) choose mapping.
- positional arguments:
BAM-FILE input file in BAM format. The output will be another BAM-FILE with the same name but prefixed with ‘parsed.’
- optional arguments:
- -h, --help
show this help message and exit
-l NUM, –min-dna-seq-length NUM
- minimum length of DNA sequence to be kept (default: 0)
- -r NUM, --min-subreads-per-molecule NUM
minimum number of subreads per molecule to keep it (default: 1)
- -q NUM, --quality-threshold NUM
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 (amount of found wanted mappings/all mappings present) in order to keep the data point (default: take all)
-v, –verbose –version show program’s version number and exit