VEP Troubleshooting

Command line

Test VEP library/annotation installation. Go to /tmp and run the following:

GRCh37

# Set to wherever you installed VG
export IN_GRCH37_VCF=~/localwork/variantgrid/annotation/tests/test_data/test_grch37.vcf

/data/annotation/VEP/ensembl-vep/vep -i ${IN_GRCH37_VCF} -o out_grch37.vcf --cache --dir /data/annotation/VEP/vep_cache --fasta /data/annotation/fasta/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --assembly GRCh37 --offline --use_given_ref --vcf --force_overwrite --flag_pick --exclude_predicted --no_stats --fork 4 --sift b --uniprot --hgvs --symbol --numbers --domains --canonical --protein --biotype --uniprot --af --pubmed --variant_class --plugin Grantham --plugin MaxEntScan,/data/annotation/VEP/annotation_data/all_builds/maxentscan --plugin SpliceRegion --plugin dbscSNV,/data/annotation/VEP/annotation_data/GRCh37/dbscSNV1.1_GRCh37.txt.gz --plugin LoFtool --plugin dbNSFP,/data/annotation/VEP/annotation_data/GRCh37/dbNSFP4.0b2a.hg19.stripped.gz,REVEL_score,MutationAssessor_pred,CADD_raw,Polyphen2_HVAR_pred,Interpro_domain,FATHMM_pred,MutationTaster_pred,GERP++_RS --custom /data/annotation/VEP/annotation_data/GRCh37/gnomad_GRCh37_combined_af.vcf.bgz,gnomAD,vcf,exact,0,AF_eas,nhomalt,gnomad_filtered,popmax,AF_asj,AF,AF_amr,AF_fin,AF_oth,AF_afr,AF_nfe,AF_popmax,AF_sas --custom /data/annotation/VEP/annotation_data/GRCh37/hg19.100way.phastCons.bw,phastCons100way_vertebrate,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh37/hg19.phastCons46way.placental.bw,phastCons46way_mammalian,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh37/hg19.100way.phyloP100way.bw,phyloP100way_vertebrate,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh37/hg19.phyloP46way.placental.bw,phyloP46way_mammalian,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh37/repeatmasker_hg19.bed.gz,REPEAT_MASKER,bed,overlap --custom /data/annotation/VEP/annotation_data/GRCh37/TOPMED_GRCh37.vcf.gz,TopMed,vcf,exact,0,TOPMED --custom /data/annotation/VEP/annotation_data/GRCh37/UK10K_COHORT.20160215.sites.vcf.gz,UK10k,vcf,exact,0,UK10K_AF

GRCh38

# Set to wherever you installed VG
export IN_GRCH38_VCF=~/localwork/variantgrid/annotation/tests/test_data/test_grch38.vcf

/data/annotation/VEP/ensembl-vep/vep -i ${IN_GRCH38_VCF} --cache --dir /data/annotation/VEP/vep_cache --fasta /data/annotation/fasta/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --assembly GRCh38 --offline --use_given_ref --vcf --force_overwrite --flag_pick --exclude_predicted --no_stats --fork 4 --sift b --uniprot --hgvs --symbol --numbers --domains --canonical --protein --biotype --uniprot --af --pubmed --variant_class --plugin Grantham --plugin MaxEntScan,/data/annotation/VEP/annotation_data/all_builds/maxentscan --plugin SpliceRegion --plugin dbscSNV,/data/annotation/VEP/annotation_data/GRCh38/dbscSNV1.1_GRCh38.txt.gz --plugin LoFtool --plugin dbNSFP,/data/annotation/VEP/annotation_data/GRCh38/dbNSFP4.0b2a.hg38.stripped.gz,REVEL_score,MutationAssessor_pred,CADD_raw,Polyphen2_HVAR_pred,Interpro_domain,FATHMM_pred,MutationTaster_pred,GERP++_RS --custom /data/annotation/VEP/annotation_data/GRCh38/gnomad_GRCh38_combined_af.vcf.bgz,gnomAD,vcf,exact,0,AF_eas,nhomalt,gnomad_filtered,popmax,AF_asj,AF,AF_amr,AF_fin,AF_oth,AF_afr,AF_nfe,AF_popmax,AF_sas --custom /data/annotation/VEP/annotation_data/GRCh38/hg38.phastCons100way.bw,phastCons100way_vertebrate,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh38/hg38.phastCons30way.bw,phastCons30way_mammalian,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh38/hg38.phyloP100way.bw,phyloP100way_vertebrate,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh38/hg38.phyloP30way.bw,phyloP30way_mammalian,bigwig,overlap --custom /data/annotation/VEP/annotation_data/GRCh38/repeatmasker_hg38.bed.gz,REPEAT_MASKER,bed,overlap --custom /data/annotation/VEP/annotation_data/GRCh38/TOPMED_GRCh38_20180418.vcf.gz,TopMed,vcf,exact,0,TOPMED --custom /data/annotation/VEP/annotation_data/GRCh38/UK10K_COHORT.20160215.sites.GRCh38.vcf.gz,UK10k,vcf,exact,0,UK10K_AF

Common problems

Error like Bio::HTS::Tabix

This can be due to conflicting libraries. Uninstall

$cpanm --uninstall Bio::Perl
$cpanm --uninstall Bio::HTS

as well as/alternatively ensemble-vep will install it's own htslib make sure that one is installed.

After running

perl INSTALL.pl --AUTO ap --PLUGINS all --CACHEDIR ${VEP_CACHE}

run

cd htslib # should now be at /data/annotation/VEP/ensembl-vep/htslib
sudo make install

# now re run
perl INSTALL.pl --AUTO ap --PLUGINS all --CACHEDIR ${VEP_CACHE}

Management commands

python3 manage.py vep_version --genome-build=GRCh37
python3 manage.py vep_run --test # will rewrite unit test imput files