Mercurial > repos > fubar > jbrowse2dev
annotate jbrowse2/convertMAF.sh @ 3:0d953fc4ca97 draft
Uploaded
| author | fubar |
|---|---|
| date | Wed, 03 Jan 2024 08:07:45 +0000 |
| parents | cd5d63cd0eb5 |
| children |
| rev | line source |
|---|---|
| 0 | 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 |