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Last pushed: a year ago
Short Description
Ensembl's Variant Effect Predictor (VEP) to determine the effect of variants on genes.
Full Description

IN THE HOST COMPUTER

(Don't need to run anything in the Docker container. Do everything in the host computer.)

Step 1. Pull the vep docker

docker pull j5kim/ensembl_vep

Step 2. Download a big vep cache file (compressed file size = 4.7 GB) to a host computer

export LOCALCACHEDIR=/Users/johndoe/MyDockers/vep/prebuiltcache

cd ${LOCALCACHEDIR}

wget ftp://ftp.ensembl.org/pub/release-84/variation/VEP/homo_sapiens_vep_84_GRCh38.tar.gz

tar -zxvf homo_sapiens_vep_84_GRCh38.tar.gz

Step 3. Download a real data for test running vep

cd ${LOCALCACHEDIR}

curl -O ftp://ftp-race.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/supplementaryfiles/NA12878_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-Solid_ALLCHROM_v3.2_all.vcf.gz

gunzip NA12878_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-Solid_ALLCHROM_v3.2_all.vcf.gz

cp NA12878_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-Solid_ALLCHROM_v3.2_all.vcf GIAB_NA12878.vcf

Step 4. Create a test run file in the HOST COMPUTER

cd ${LOCALCACHEDIR}

echo -e "cd /opt/vep/ensembl-tools-release-84/scripts/variant_effect_predictor" > testrun.sh

echo -e "perl variant_effect_predictor.pl --cache --dir /root/.vep -i /root/.vep/GIAB_NA12878.vcf -o /root/.vep/output_GIAB_NA12878.txt --chr 21 --coding_only" >> testrun.sh

Step 5. Run docker with a real example, Genome In A Bottle (GIAB) NA12878 vcf file as an input

cd ${LOCALCACHEDIR}

docker run -i -t -m 4g -v ${LOCALCACHEDIR}:/root/.vep j5kim/ensembl_vep:v0.1 /bin/bash /root/.vep/testrun.sh

Reference:

Zook et al, Nat Biotech, 2014 (http://www.nature.com/nbt/journal/v32/n3/full/nbt.2835.html)
Extensive sequencing of seven human genomes to characterize benchmark reference materials
PMID = 24531798

https://docs.google.com/spreadsheets/d/1iL45zPit9-kVmk-9sDJEGMhxsUWf52n1nw_duTdNwcE/edit?pref=2&pli=1#gid=0
https://sites.stanford.edu/abms/content/giab-reference-materials-and-data

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j5kim

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