Mercurial > repos > fubar > jbrowse2
view convertMAF.sh @ 14:7c2e28e144f3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776
author | fubar |
---|---|
date | Mon, 22 Jan 2024 12:05:09 +0000 |
parents | d78175596286 |
children | 94264fe60478 |
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#!/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