Mercurial > repos > fubar > jbrowse2dev
view jbrowse2/convertMAF.sh @ 9:6a41f87b5d7f draft
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author | fubar |
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date | Fri, 05 Jan 2024 05:06:21 +0000 |
parents | cd5d63cd0eb5 |
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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