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replace run-gen-hs38* with run-gen-ref

This commit is contained in:
Heng Li 2014-11-16 00:46:02 -05:00
parent 050482ef77
commit 792be78a80
3 changed files with 31 additions and 18 deletions
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9
extras/run-gen-hs38a
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@ -1,9 +0,0 @@
#!/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"

9
extras/run-gen-hs38d6
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@ -1,9 +0,0 @@
#!/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"

31
extras/run-gen-ref 100755
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@ -0,0 +1,31 @@
#!/bin/bash
root=`dirname $0`
url38="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"
url37d5="ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz"
if [ $# -eq 0 ]; then
echo "Usage: $0 <hs38|hs38a|hs38d6|hs37|hs37d5>"
exit 1;
fi
if [ $1 == "hs38d6" ]; then
(wget -O- $url38 | gzip -dc; cat $root/resource-GRCh38/hs38d6-extra.fa) > $1.fa
[ ! -f $1.fa.alt ] && cp $root/resource-GRCh38/hs38d6.fa.alt $1.fa.alt
elif [ $1 == "hs38a" ]; then
wget -O- $url38 | gzip -dc > $1.fa
[ ! -f $1.fa.alt ] && grep _alt $root/resource-GRCh38/hs38d6.fa.alt > $1.fa.alt
elif [ $1 == "hs38" ]; then
# we don't use GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz because it lacks EBV
wget -O- $url38 | gzip -dc | awk '/^>/{f=/_alt/?0:1}f' > $1.fa
elif [ $1 == "hs37d5" ]; then
wget -O- $url37d5 | gzip -dc > $1.fa 2>/dev/null
elif [ $1 == "hs37" ]; then
wget -O- $url37d5 | gzip -dc 2>/dev/null | awk '/^>/{f=/>hs37d5/?0:1}f' > $1.fa
else
echo "ERROR: unknown genome build"
fi
[ ! -f $1.fa.bwt ] && echo -e "\nPlease run 'bwa index $1.fa'...\n"