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bedtools BED to BAM (version 2.30.0+galaxy1)

Convert the following BED file to BAM:

Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format:

If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string

Genome file:

Set a mapping quality (SAM MAPQ field) value for all BED entries:

What it does

bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes.

This tool is part of the bedtools package from the Quinlan laboratory.

Citation

If you use this tool in Galaxy, please cite:

Bjoern A. Gruening (2014), Galaxy wrapper