Installing and running Ensembl VEP via vcf2maf

README.md

Instructions

These instructions are intended for Linux.

1. Install Miniconda 3.
2. Create conda environment using the attached environment.yml file:

   conda env create -n vep -f environment.yml

3. Download VEP cache and decompress the TAR archive:

   mkdir ~/vep_cache
   rsync -avh --progress rsync://ftp.ensembl.org/ensembl/pub/release-103/variation/indexed_vep_cache/homo_sapiens_vep_103_GRCh38.tar.gz ~/vep_cache/homo_sapiens_vep_103_GRCh38.tar.gz
   tar vxzf ~/vep_cache/homo_sapiens_vep_103_GRCh38.tar.gz

4. Pre-load VEP cache into memory:

   rsync -avhP ~/vep_cache/ /dev/shm/vep_cache/

5. Activate VEP conda environment and run attached Bash script:

   conda activate vep
   bash ./run-vcf2maf.sh /path/to/sample.vcf.gz

environment.yml

name: vep
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1
  - _openmp_mutex=4.5
  - atk-1.0=2.36.0
  - bzip2=1.0.8
  - c-ares=1.17.1
  - ca-certificates=2020.12.5
  - cairo=1.16.0
  - certifi=2020.12.5
  - clustalw=2.1
  - curl=7.76.1
  - ensembl-vep=103.1
  - expat=2.3.0
  - font-ttf-dejavu-sans-mono=2.37
  - font-ttf-inconsolata=3.000
  - font-ttf-source-code-pro=2.038
  - font-ttf-ubuntu=0.83
  - fontconfig=2.13.1
  - fonts-conda-ecosystem=1
  - fonts-conda-forge=1
  - freetype=2.10.4
  - fribidi=1.0.10
  - gdk-pixbuf=2.42.6
  - gettext=0.19.8.1
  - giflib=5.2.1
  - graphite2=1.3.13
  - graphviz=2.47.1
  - gtk2=2.24.33
  - gts=0.7.6
  - harfbuzz=2.8.1
  - htslib=1.10.2
  - icu=68.1
  - jpeg=9d
  - krb5=1.17.2
  - ld_impl_linux-64=2.35.1
  - libcurl=7.76.1
  - libdb=6.2.32
  - libdeflate=1.6
  - libedit=3.1.20191231
  - libev=4.33
  - libffi=3.3
  - libgcc-ng=9.3.0
  - libgd=2.3.2
  - libglib=2.68.1
  - libgomp=9.3.0
  - libiconv=1.16
  - libnghttp2=1.43.0
  - libpng=1.6.37
  - librsvg=2.50.3
  - libssh2=1.9.0
  - libstdcxx-ng=9.3.0
  - libtiff=4.2.0
  - libtool=2.4.6
  - libuuid=2.32.1
  - libwebp=1.2.0
  - libwebp-base=1.2.0
  - libxcb=1.13
  - libxml2=2.9.10
  - libxslt=1.1.33
  - lz4-c=1.9.3
  - mysql-connector-c=6.1.11
  - ncurses=6.2
  - openssl=1.1.1k
  - paml=4.9
  - pango=1.42.4
  - pcre=8.44
  - perl=5.26.2
  - perl-aceperl=1.92
  - perl-algorithm-diff=1.1903
  - perl-algorithm-munkres=0.08
  - perl-apache-test=1.40
  - perl-app-cpanminus=1.7044
  - perl-appconfig=1.71
  - perl-array-compare=3.0.1
  - perl-autoloader=5.74
  - perl-base=2.23
  - perl-bio-asn1-entrezgene=1.73
  - perl-bio-coordinate=1.007001
  - perl-bio-db-hts=3.01
  - perl-bio-featureio=1.6.905
  - perl-bio-phylo=0.58
  - perl-bio-samtools=1.43
  - perl-bio-tools-phylo-paml=1.7.3
  - perl-bio-tools-run-alignment-clustalw=1.7.4
  - perl-bio-tools-run-alignment-tcoffee=1.7.4
  - perl-bioperl=1.7.2
  - perl-bioperl-core=1.007002
  - perl-bioperl-run=1.007002
  - perl-business-isbn=3.004
  - perl-business-isbn-data=20140910.003
  - perl-cache-cache=1.08
  - perl-capture-tiny=0.48
  - perl-carp=1.38
  - perl-cgi=4.44
  - perl-class-data-inheritable=0.08
  - perl-class-inspector=1.34
  - perl-class-load=0.25
  - perl-class-load-xs=0.10
  - perl-class-method-modifiers=2.12
  - perl-clone=0.42
  - perl-common-sense=3.74
  - perl-compress-raw-bzip2=2.087
  - perl-compress-raw-zlib=2.087
  - perl-constant=1.33
  - perl-convert-binary-c=0.78
  - perl-convert-binhex=1.125
  - perl-crypt-rc4=2.02
  - perl-data-dumper=2.173
  - perl-data-optlist=0.110
  - perl-data-stag=0.14
  - perl-date-format=2.30
  - perl-db-file=1.855
  - perl-dbd-mysql=4.046
  - perl-dbd-sqlite=1.64
  - perl-dbi=1.642
  - perl-devel-globaldestruction=0.14
  - perl-devel-overloadinfo=0.005
  - perl-devel-stacktrace=2.04
  - perl-digest-hmac=1.03
  - perl-digest-md5=2.55
  - perl-digest-perl-md5=1.9
  - perl-digest-sha1=2.13
  - perl-dist-checkconflicts=0.11
  - perl-dynaloader=1.25
  - perl-email-date-format=1.005
  - perl-encode=2.88
  - perl-encode-locale=1.05
  - perl-error=0.17027
  - perl-eval-closure=0.14
  - perl-exception-class=1.44
  - perl-exporter=5.72
  - perl-exporter-tiny=1.002001
  - perl-extutils-makemaker=7.36
  - perl-file-listing=6.04
  - perl-file-path=2.16
  - perl-file-slurp-tiny=0.004
  - perl-file-sort=1.01
  - perl-file-temp=0.2304
  - perl-file-which=1.23
  - perl-font-afm=1.20
  - perl-font-ttf=1.06
  - perl-gd=2.68
  - perl-getopt-long=2.50
  - perl-graph=0.9704
  - perl-graphviz=2.24
  - perl-html-element-extended=1.18
  - perl-html-entities-numbered=0.04
  - perl-html-formatter=2.16
  - perl-html-parser=3.72
  - perl-html-tableextract=2.13
  - perl-html-tagset=3.20
  - perl-html-tidy=1.60
  - perl-html-tree=5.07
  - perl-html-treebuilder-xpath=0.14
  - perl-http-cookies=6.04
  - perl-http-daemon=6.01
  - perl-http-date=6.02
  - perl-http-message=6.18
  - perl-http-negotiate=6.01
  - perl-image-info=1.38
  - perl-image-size=3.300
  - perl-io-compress=2.087
  - perl-io-html=1.001
  - perl-io-sessiondata=1.03
  - perl-io-socket-ssl=2.066
  - perl-io-string=1.08
  - perl-io-stringy=2.111
  - perl-io-tty=1.12
  - perl-ipc-run=20180523.0
  - perl-ipc-sharelite=0.17
  - perl-jcode=2.07
  - perl-json=4.02
  - perl-json-xs=2.34
  - perl-lib=0.63
  - perl-libwww-perl=6.39
  - perl-libxml-perl=0.08
  - perl-list-moreutils=0.428
  - perl-list-moreutils-xs=0.428
  - perl-lwp-mediatypes=6.04
  - perl-lwp-protocol-https=6.07
  - perl-lwp-simple=6.15
  - perl-mailtools=2.21
  - perl-math-cdf=0.1
  - perl-math-derivative=1.01
  - perl-math-random=0.72
  - perl-math-spline=0.02
  - perl-mime-base64=3.15
  - perl-mime-lite=3.030
  - perl-mime-tools=5.508
  - perl-mime-types=2.17
  - perl-mldbm=2.05
  - perl-module-implementation=0.09
  - perl-module-runtime=0.016
  - perl-module-runtime-conflicts=0.003
  - perl-moo=2.003004
  - perl-moose=2.2011
  - perl-mozilla-ca=20180117
  - perl-mro-compat=0.13
  - perl-net-http=6.19
  - perl-net-ssleay=1.88
  - perl-ntlm=1.09
  - perl-ole-storage_lite=0.19
  - perl-package-deprecationmanager=0.17
  - perl-package-stash=0.38
  - perl-package-stash-xs=0.28
  - perl-params-util=1.07
  - perl-parent=0.236
  - perl-parse-recdescent=1.967015
  - perl-pathtools=3.75
  - perl-pdf-api2=2.035
  - perl-perlio-gzip=0.20
  - perl-pod-escapes=1.07
  - perl-pod-usage=1.69
  - perl-postscript=0.06
  - perl-role-tiny=2.000008
  - perl-scalar-list-utils=1.52
  - perl-sereal=4.007
  - perl-sereal-decoder=4.007
  - perl-sereal-encoder=4.007
  - perl-set-intervaltree=0.12
  - perl-set-scalar=1.29
  - perl-soap-lite=1.19
  - perl-socket=2.027
  - perl-sort-naturally=1.03
  - perl-spreadsheet-parseexcel=0.65
  - perl-spreadsheet-writeexcel=2.40
  - perl-statistics-descriptive=3.0702
  - perl-storable=3.15
  - perl-sub-exporter=0.987
  - perl-sub-exporter-progressive=0.001013
  - perl-sub-identify=0.14
  - perl-sub-install=0.928
  - perl-sub-name=0.21
  - perl-sub-quote=2.006003
  - perl-sub-uplevel=0.2800
  - perl-svg=2.84
  - perl-svg-graph=0.02
  - perl-task-weaken=1.06
  - perl-template-toolkit=2.26
  - perl-test=1.26
  - perl-test-deep=1.128
  - perl-test-differences=0.67
  - perl-test-exception=0.43
  - perl-test-harness=3.42
  - perl-test-leaktrace=0.16
  - perl-test-most=0.35
  - perl-test-requiresinternet=0.05
  - perl-test-warn=0.36
  - perl-text-csv=2.00
  - perl-text-diff=1.45
  - perl-tie-ixhash=1.23
  - perl-time-hires=1.9760
  - perl-time-local=1.28
  - perl-timedate=2.30
  - perl-tree-dag_node=1.31
  - perl-try-tiny=0.30
  - perl-type-tiny=1.004004
  - perl-types-serialiser=1.0
  - perl-unicode-map=0.112
  - perl-uri=1.76
  - perl-www-robotrules=6.02
  - perl-xml-dom=1.46
  - perl-xml-dom-xpath=0.14
  - perl-xml-filter-buffertext=1.01
  - perl-xml-libxml=2.0132
  - perl-xml-libxslt=1.94
  - perl-xml-namespacesupport=1.12
  - perl-xml-parser=2.44_01
  - perl-xml-regexp=0.04
  - perl-xml-sax=1.02
  - perl-xml-sax-base=1.09
  - perl-xml-sax-expat=0.51
  - perl-xml-sax-writer=0.57
  - perl-xml-simple=2.25
  - perl-xml-twig=3.52
  - perl-xml-writer=0.625
  - perl-xml-xpath=1.44
  - perl-xml-xpathengine=0.14
  - perl-xsloader=0.24
  - perl-yaml=1.29
  - pip=21.1.1
  - pixman=0.40.0
  - pthread-stubs=0.4
  - python=3.7.10
  - python_abi=3.7
  - readline=8.1
  - samtools=1.10
  - setuptools=49.6.0
  - sqlite=3.35.5
  - t_coffee=11.0.8
  - tidyp=1.04
  - tk=8.6.10
  - unzip=6.0
  - vcf2maf=1.6.20
  - wheel=0.36.2
  - xorg-kbproto=1.0.7
  - xorg-libice=1.0.10
  - xorg-libsm=1.2.3
  - xorg-libx11=1.7.0
  - xorg-libxau=1.0.9
  - xorg-libxdmcp=1.1.3
  - xorg-libxext=1.3.4
  - xorg-libxrender=0.9.10
  - xorg-renderproto=0.11.1
  - xorg-xextproto=7.3.0
  - xorg-xproto=7.0.31
  - xz=5.2.5
  - zlib=1.2.11
  - zstd=1.4.9
  

run-vcf2maf.sh

#!/bin/bash

set -euf -o pipefail

INPUT_VCF="${1}"

# Decompress VCF file, if applicable
if [[ $INPUT_VCF == *.gz ]]; then
    INPUT_VCF_DECOMP=${INPUT_VCF/%.vcf.gz/.vcf}
    >&2 echo "Decompressing VCF file: $INPUT_VCF > $INPUT_VCF_DECOMP"
    gzip -dc $INPUT_VCF > $INPUT_VCF_DECOMP
    INPUT_VCF=$INPUT_VCF_DECOMP
fi

INTER_VCF="${INPUT_VCF/%.vcf/.pass.vcf}"
INTER_VEP_VCF="${INTER_VCF/%.vcf/.vep.vcf}"
OUTPUT_MAF="${INPUT_VCF/%.vcf/.pass.maf}"
LOGS_DIR="$(dirname ${INPUT_VCF})/logs"
LOGS_PREFIX="$LOGS_DIR/$(basename ${INPUT_VCF} .vcf)"

mkdir -p "$LOGS_DIR"

>&2 echo "Filtering for passed variants: $INPUT_VCF > $INTER_VCF"
awk 'BEGIN {FS=OFS="\t"} $0 ~ /^#/ || $7 == "PASS" || $7 == "."' "$INPUT_VCF" > "$INTER_VCF"

>&2 echo "Converting VCF to MAF: $INTER_VCF > $OUTPUT_MAF"
rm -f "$INTER_VEP_VCF" "$OUTPUT_MAF"
vcf2maf.pl \
    --input-vcf "$INTER_VCF" \
    --output-maf "$OUTPUT_MAF" \
    --vep-path ~/miniconda3/envs/vep/share/ensembl-vep-103.1-2/ \
    --vep-data /dev/shm/vep_cache/ \
    --vep-forks 6 \
    --species homo_sapiens \
    --ncbi-build GRCh38 \
    --cache-version 103 \
    --maf-center "Sage Bionetworks" \
    > "$LOGS_PREFIX.out" \
    2> "$LOGS_PREFIX.err"

>&2 echo "Logs will be here:"
>&2 echo "- stdout: $LOGS_PREFIX.out"
>&2 echo "- stderr: $LOGS_PREFIX.err"