Skip to content

Instantly share code, notes, and snippets.

@knmkr

knmkr/download_human_fasta.sh

Created July 9, 2016 14:32
Show Gist options
  • Save knmkr/e38b4ef07dff3884885c1fa7a141016f to your computer and use it in GitHub Desktop.
Save knmkr/e38b4ef07dff3884885c1fa7a141016f to your computer and use it in GitHub Desktop.
Download ZIP
misc.
Raw
download_human_fasta.sh
# GRCh37.p13
# $ wget -r ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/Primary_Assembly/assembled_chromosomes/FASTA/
# $ for x in {1..22} X Y; do gzip -dc chr${x}.fa.gz >> GRCh37.p13.fa; done
# UCSC hg18 (Build36.1) -- http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/
# $ wget -r -l1 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/'
# $ for x in {1..22} X Y; do gzip -dc hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr${x}.fa.gz >> hg18.fa; done
# UCSC hg17 (Build35) -- http://hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/
# $ wget -r -l1 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/'
# $ for x in {1..22} X Y; do gzip -dc hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/chr${x}.fa.gz >> hg17.fa; done
@knmkr
Copy link
Author

knmkr commented Jul 10, 2016 •
edited
Loading 

$ tabix -p vcf file.vcf.bgz

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment