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added scripts to generate hs38a.fa and hs38d6.fa

This commit is contained in:
Heng Li 2014-11-13 12:53:29 -05:00
parent fffe52a45b
commit a5c144db4d
3 changed files with 18 additions and 0 deletions
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extras/run-HLA.sh → extras/run-HLA
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extras/run-gen-hs38a 100755
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#!/bin/bash
root=`dirname $0`
wget -O- ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz \
| gzip -dc > hs38a.fa
[ ! -f hs38a.fa.alt ] && grep _alt $root/resource-GRCh38/hs38d6.fa.alt > hs38a.fa.alt
[ ! -f hs38a.fa.bwt ] && echo -e "\nPlease run 'bwa index hs38a.fa'...\n"

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extras/run-gen-hs38d6 100755
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#!/bin/bash
root=`dirname $0`
(wget -O- ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz \
| gzip -dc; cat $root/data/hs38d6-extra.fa) > hs38d6.fa
[ ! -f hs38d6.fa.alt ] && cp $root/resource-GRCh38/hs38d6.fa.alt .
[ ! -f hs38d6.fa.bwt ] && echo -e "\nPlease run 'bwa index hs38d6.fa'...\n"