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Filter SAM or BAM, output SAM or BAM (version 1.8+galaxy1)

SAM or BAM file to filter:

Header in output:

Minimum MAPQ quality score:

(-q)

Filter on bitwise flag:

Select alignments from Library:

(-l) Requires headers in the input SAM or BAM, otherwise no alignments will be output

Select alignments from Read Group:

(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output

Output alignments overlapping the regions in the BED file:

(-L)

Use inverse selection:

Select the opposite of the listed chromosomes

Select regions (only used when the input is in BAM format):

region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'

Select the output format:

What it does

This tool uses the samtools view command in SAMtools toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.

Input

Input is either a SAM or BAM file.

Output

The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.

Options

Filtering by read group or library requires headers in the input SAM or BAM file.

If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions. A region can be presented, for example, in the following format:

chr2  (the whole chr2)
chr2:1000000   (region starting from 1,000,000bp)
chr2:1,000,000-2,000,000      (region between 1,000,000 and 2,000,000bp including the end points).

Note: The coordinate is 1-based.

Multiple regions may be specified, separated by a space character:

chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX