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annotate jbrowse2/convertMAF.sh @ 4:52842c3f2dda draft

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author fubar
date Wed, 03 Jan 2024 23:27:23 +0000
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1 #!/usr/bin/env bash
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2 # https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
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3 # MAF file must contain the species name and chromosome name
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4 # e.g. hg38.chr1 in the sequence identifiers.
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5 perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
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6 bgzip $4.sorted.bed
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7 tabix -p bed $4.sorted.bed.gz