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| #!/bin/bash | |
| # usage: refdiff.sh <h37>.bed <hg19>.bed | |
| bedtools getfasta -fi /resources/h37/human_g1k_v37.fasta -bed $1 -fo - | sed -e 's/MT/M/' | tr '[:lower:]' '[:upper:]' > tmp.h37.fasta | |
| bedtools getfasta -fi /resources/hg19/ucsc.hg19.fasta -bed $2 -fo - | sed -e 's/chr//' | tr '[:lower:]' '[:upper:]' > tmp.hg19.fasta | |
| diff -u tmp.h*.fasta | |
| rm tmp.h*.fasta |
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