comparison jbrowse2/convertMAF.sh @ 0:cd5d63cd0eb5 draft

Uploaded
author fubar
date Wed, 03 Jan 2024 01:36:39 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:cd5d63cd0eb5
1 #!/usr/bin/env bash
2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
3 # MAF file must contain the species name and chromosome name
4 # e.g. hg38.chr1 in the sequence identifiers.
5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
6 bgzip $4.sorted.bed
7 tabix -p bed $4.sorted.bed.gz