Hi all,
I’m a beginner in Hail. I was wondering if it is possible to annotate from custom file/sources when using ‘vep’ function in Hail.
Thanks in advance!
Hi all,
I’m a beginner in Hail. I was wondering if it is possible to annotate from custom file/sources when using ‘vep’ function in Hail.
Thanks in advance!
I think I don’t completely understand what you’re looking to do. It’s not possible to run VEP with different configurations / plugins than we expose in the method parameters (e.g. CSQ vs the full json schema). However, it’s absolutely possible to annotate from text files like .bed / interval files, VCFs, or arbitrary delimited text files.
Can you share what those custom files/sources look like?
Hi,
I have annotated some VCF files with VEP using the below script:
#!/bin/bash
set -e
set -u
set -o pipefail
cd ~/projects/wes_10k
for inputfile in test_data/*.vcf.gz
do
outfile=$(basename "$inputfile")
outfile="${outfile%.*}"
echo "processing file: $inputfile ..."
perl ./vep -i "$inputfile" -o ./vep_annotated/"$outfile.gz" \
--fork 24 \
--cache \
--offline \
--cache_version 90 \
--custom ~/.vep/annotation/gonl.SV.r5.vcf.gz,GONL,vcf,exact,0,AF \
--custom ~/.vep/annotation/anon-SweGen_STR_NSPHS_1000samples_freq_hg19.vcf.gz,SWEGEN,vcf,exact,0,AF \
--custom ~/.vep/annotation/gnomad.exomes.r2.0.1.sites.noVEP.vcf.gz,GNOMAD,vcf,exact,0,AF \
--custom ~/.vep/annotation/ExAC.0.3.GRCh37.vcf.gz,ExAC,vcf,exact,0,AF \
--custom ~/.vep/annotation/conserved_sorted_cleaned.bed.gz,CONSERVED,bed,overlap,0 \
--custom ~/.vep/annotation/ddd-unaffected-parental-maf-2017-03-18.bed.gz,DDD_PARENT,bed,overlap,0 \
--custom ~/.vep/annotation/enhancer_sorted_cleaned.bed.gz,ENHANCER,bed,overlap,0 \
--custom ~/.vep/annotation/ESP6500SI_21012013_MAF.bed.gz,ESP6500SI,bed,overlap,0 \
--custom ~/.vep/annotation/heart_sorted_cleaned.bed.gz,ENH_HEART,bed,overlap,0 \
--custom ~/.vep/annotation/segmentaldup_USCS_hg19_sorted_cleaned.bed.gz,SEGMENTAL_DUP,bed,overlap,0 \
--custom ~/.vep/annotation/TRF_USCS_hg19_sorted_cleaned.bed.gz,TRF,bed,overlap,0 \
--custom ~/.vep/annotation/UK10K_COHORT_20130116_AF.bed.gz,UK10K,bed,overlap,0 \
--flag_pick --vcf --force_overwrite --compress_output bgzip
done
But I would like to integrate this step also into my Hail workflow. So, Can I run Vep into Hail using the same settings?
Thanks
No, this won’t work
It’s hard to make VEP totally customizable in Hail, because we need to know what the schema of the resulting annotations is. VEP doesn’t make it easy to know / guess that, so we’ve had to guess and check it for the standard+LOFTEE setup (the Hail supports).
It would certainly be possible to run this yourself on the sites files, and join with the multi-sample VCFs later.
I see, many thanks for your quick reply. Anyhow, Hail allows me to parse/process really well these annotations later in the workflow!
Thanks again!