From ef0607d684e4e0c512a37ac1d607134bb439f9f8 Mon Sep 17 00:00:00 2001 From: Agnieszka Danek Date: Thu, 10 Mar 2016 07:46:13 +0100 Subject: [PATCH] Update of NCBI path to reference sequences (run) On 02-DEC-2015 all content of ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/ was moved to ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank --- vcf2fasta/run | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/vcf2fasta/run b/vcf2fasta/run index 9a082de..8d486b6 100755 --- a/vcf2fasta/run +++ b/vcf2fasta/run @@ -60,7 +60,7 @@ download() if [ -f chrX.fa.gz ]; then rm chrX.fa.gz fi - wget -nv ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/chrX.fa.gz + wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/chrX.fa.gz echo "*** Decompressing reference sequence for chr X ***" gzip -d chrX.fa.gz X_downloaded="1" @@ -71,7 +71,7 @@ download() rm chrY.fa.gz fi - wget -nv ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/chrY.fa.gz + wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/chrY.fa.gz echo "*** Decompressing reference sequence for chr Y ***" gzip -d chrY.fa.gz @@ -86,7 +86,7 @@ download() rm chr$c.fa.gz fi - wget -nv ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/chr$c.fa.gz + wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/Primary_Assembly/assembled_chromosomes/FASTA/chr$c.fa.gz echo "*** Decompressing reference sequence for chr $c ***" gzip -d chr$c.fa.gz