Mercurial > repos > fubar > jbrowse2
view convertMAF.sh @ 32:fe48ed5810bd draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
author | fubar |
---|---|
date | Fri, 23 Feb 2024 07:24:58 +0000 |
parents | d78175596286 |
children | 94264fe60478 |
line wrap: on
line source
#!/usr/bin/env bash # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh # MAF file must contain the species name and chromosome name # e.g. hg38.chr1 in the sequence identifiers. perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed bgzip $4.sorted.bed tabix -p bed $4.sorted.bed.gz