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SNPeff ENSEMBL 102 database construction , vep-102 installation and separate vep annotation by species to avoid human only option issues #10

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SNPeff ENSEMBL 102 database construction , vep-102 installation and separate vep annotation by species to avoid human only option issues #10

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5ba48d5
Add custom SNPeff database with ENSEMBL 102 data and vep-102 installa…
Jan 31, 2022
0ecc1b7
separate vep command for mouse and human because polyphen and gnomad …
Just08 Jan 31, 2022
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37 changes: 36 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ ENV LC_ALL=en_US.UTF-8

ENV PATH ${PATH}:${PACKAGE_DIR}/bin

ENV PERL5LIB ${PACKAGE_DIR}/vep-96:${PERL5LIB}
ENV PERL5LIB ${PACKAGE_DIR}/vep-96:${PACKAGE_DIR}/vep-102:${PERL5LIB}

## Configure default locale, mostly to avoid problems with R (sorting etc.),
## see https://github.com/rocker-org/rocker/issues/19
Expand Down Expand Up @@ -380,6 +380,32 @@ RUN cd ${TEMP_DIR} \
&& rm snpEff_v4_3_GRCm38.86.zip \
&& rm -r snpEff_v4_3_GRCm38.86

# SnpEff mouse database update
RUN cd ${TEMP_DIR} \
&& wget -nv http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz \
&& mkdir -p ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102 \
&& mv Mus_musculus.GRCm38.102.gtf.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/genes.gtf.gz \
&& wget -nv http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/pep/Mus_musculus.GRCm38.pep.all.fa.gz \
&& mv Mus_musculus.GRCm38.pep.all.fa.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/protein.fa.gz \
&& wget -nv http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz \
&& mv Mus_musculus.GRCm38.cdna.all.fa.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/cds.fa.gz \
&& wget -nv http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz \
&& mv Mus_musculus.GRCm38.dna.toplevel.fa.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/sequences.fa.gz \
&& gunzip ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/*.gz \
# && curl -H 'Accept: text/pfm' -X GET "https://jaspar.genereg.net/api/v1/species/10090/?version=1&release=2022&page=1&page_size=1000&collection=CORE" > pfm_all_mouse.txt \
# && gzip -c pfm_all_mouse.txt > ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/pwms.bin \
# && wget -nv http://ftp.ensembl.org/pub/release-102/regulation/mus_musculus/MotifFeatures/Mus_musculus.GRCm38.motif_features.gff.gz \
# && mv Mus_musculus.GRCm38.motif_features.gff.gz ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/motif.gff.gz \
# && gunzip ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/motif.gff.gz \
&& echo 'GRCm38.102.genome : Mus_musculus' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
&& echo 'GRCm38.102.reference : ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/' >> ${PACKAGE_DIR}/snpEff-4.3T/snpEff.config \
&& java -Xmx20g -jar ${PACKAGE_DIR}/snpEff-4.3T/snpEff.jar build -v GRCm38.102 \
&& rm ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/genes.gtf \
&& rm ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/protein.fa \
&& rm ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/cds.fa \
&& rm ${PACKAGE_DIR}/snpEff-4.3T/data/GRCm38.102/sequences.fa
# && rm pfm_all_mouse.txt

# Trimmomatic v0.39 (http://www.usadellab.org)
RUN cd ${TEMP_DIR} \
&& wget -nv 'http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip' \
Expand Down Expand Up @@ -474,6 +500,15 @@ RUN cd ${TEMP_DIR} \
&& mv ensembl-vep ${PACKAGE_DIR}/vep-96 \
&& perl ${PACKAGE_DIR}/vep-96/INSTALL.pl --AUTO a --DESTDIR ${PACKAGE_DIR}/vep-96 --NO_UPDATE --NO_TEST --NO_HTSLIB

# Ensembl VEP 102.0 (https://github.com/Ensembl/ensembl-vep.git)
RUN cd ${TEMP_DIR} \
&& git clone 'https://github.com/Ensembl/ensembl-vep.git' \
&& cd ensembl-vep \
&& git checkout 'release/102.0' \
&& cd ${TEMP_DIR} \
&& mv ensembl-vep ${PACKAGE_DIR}/vep-102 \
&& perl ${PACKAGE_DIR}/vep-102/INSTALL.pl --AUTO a --DESTDIR ${PACKAGE_DIR}/vep-102 --NO_UPDATE --NO_TEST --NO_HTSLIB

# vcf2maf 1.6.17 (https://github.com/mskcc/vcf2maf/archive/v1.6.17.tar.gz)
RUN cpanm --notest LWP::Simple Archive::Zip Archive::Extract HTTP::Tiny Test::Simple File::Copy::Recursive Perl::OSType Module::Metadata version TAP::Harness CGI Encode CPAN::Meta JSON DBD::SQLite Set::IntervalTree Archive::Tar Time::HiRes Module::Build Bio::Root::Version \
&& cd ${TEMP_DIR} \
Expand Down
21 changes: 21 additions & 0 deletions repository/SNV_StrelkaPostprocessing.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,9 @@ do
# echo "0 $method mutations found in $name.Strelka.$method.vcf"
# continue
# fi


if [ $species = 'homo_sapiens' ]; then

$vep_dir/./vep --cache --species $species \
-i $name/results/Strelka/$name.Strelka.$method.vcf \
Expand All @@ -114,6 +117,24 @@ do
--fork 4 --cache_version $chacheVersion --polyphen b --af --af_1kg --af_esp \
--af_gnomad --force_overwrite --dir $vepdata_dir

elif [ $species = 'mus_musculus' ]; then

$vep_dir/./vep --cache --species $species \
-i $name/results/Strelka/$name.Strelka.$method.vcf \
-o $name/results/Strelka/$name.Strelka.$method.vep.vcf \
--fasta $genome_file --assembly $assembly \
--offline --no_progress --no_stats \
--buffer_size 5000 --sift b --ccds --uniprot --hgvs \
--symbol --numbers --domains --gene_phenotype --canonical \
--protein --biotype --uniprot --tsl --pubmed --variant_class \
--shift_hgvs 1 --check_existing --total_length --allele_number \
--no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele \
--pick_order canonical,tsl,biotype,rank,ccds,length --format vcf \
--fork 4 --cache_version $chacheVersion --af --af_1kg --af_esp \
--force_overwrite --dir $vepdata_dir

fi

# --> adding cache_version 96 and --dir fixes the issues!

perl $vcf2maf_dir/vcf2maf.pl \
Expand Down