| pairedBamToBed12 converts properly paired BAM alignments to BED12 format. Typical proper pairs will be represented by a 2 blocks BED12 entry. Additional blocks are produced when an alignment contains long deletion (CIGAR N-op). Thickness indicates the first read of the pair. The BAM input file must be grouped/sorted by query name (not alignment position).
Source:https://github.com/Population-Transcriptomics/pairedBamToBed12 |
hg clone https://toolshed.g2.bx.psu.edu/repos/brenninc/pairedbamtobed12
| Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required) |
| Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required) |
| Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required) |
| Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required) |
| Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc (prior install required) |
| Name | Version | Type | |
|---|---|---|---|
| pairedbamtobed12 | 1.0 | package | |
| samtools | 1.2 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Paired Bam to Bed. With samtools sorting by name beforehand and back to required order for galaxy afterwards. | 0.1 | any | |