A utility tool to filter alignments from bam files, using identity percent, low complexity and read coverage.
bamFilters -h
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v-2019.01.22.0
compiled with dynamic htslib from samtools/1.10.2
Usage: bamFilters -b <in.bam> -o <out.bma> [-u <out.uniq.bam>] [options]
Options: -b FILE input BAM file
-o FILE output BAM file
-i INT identity percent level, default is 0
-p output identity percent in the XI tag, default is off
-a INT alignment percent level, default is 0
-r INT filter out sequences which contain more than r% of low-complexity bases, default is 100%
-n INT filter out sequences which contain less than n high-complexity bases, default is 0
-s INT don't count deletions longer than s as parts of alignment (useful for spliced mapping)
-u FILE output BAM file for uniq filter which select reads that mapped only at one position
-z bam files no genereted, only list of sequences names of reference with one or more match.
No compatible with -u and -o. print on stdout
-y FILE produce stats files with percent id, ali for each alignement
-v verbose mode
-h help
Example : bamFilters -b ./in.bam -i 95 -a 80 -r 75 -n 30 -o ./out.bam -u ./out.filter.bam