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