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CUSTOM_GNOMAD_REF.md

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Custom gnomAD Reference Creation

This documentation outlines how we created our gnomAD annotation reference. While the gnomAD source itself is very large and comprehensive, this reference is meant to add the "bare minimum" as a useful start for variant filtering out-of-the-box with a called VCF. The main steps for reference creation are:

  1. Download and pipe to bcftools and vt to grab desired fields and to normalize calls (see https://genome.sph.umich.edu/wiki/Vt#Normalization)
  2. Use pysam to add custom fields including an INFO field for the FILTER value from the source file, a popmax AF for non-cancer populations with no bottlenecks (as defined here) and a popmax with bottleneck populations
  3. Create an echtvar reference for blazing fast annotation of VCF files with this custom reference

Download and normalize

Used docker image pgc-images.sbgenomics.com/d3b-bixu/vcfutils:latest, installed curl. Desired fields to subset from gnomAD are as follows:

AC
AN
AF
nhomalt
AC_popmax
AN_popmax
AF_popmax
nhomalt_popmax
AC_controls_and_biobanks
AN_controls_and_biobanks
AF_controls_and_biobanks
AF_non_cancer
primate_ai_score
splice_ai_consequence
AF_non_cancer_afr
AF_non_cancer_ami
AF_non_cancer_asj
AF_non_cancer_eas
AF_non_cancer_fin
AF_non_cancer_mid
AF_non_cancer_nfe
AF_non_cancer_oth
AF_non_cancer_raw
AF_non_cancer_sas
AF_non_cancer_amr

Example command: Created a chromosome chr1-22,X,Y list and used xargs to run this script

cat chr_list | xargs -IFN -P 12 scripts/dl_subset_gnomad.sh FN

Add GNOMAD_FILTER, AF_non_cancer_popmax, and AF_non_cancer_all_popmax INFO fields

Use scripts/custom_vcf_info.py to add new custom fields, calculated as follows:

  • GNOMAD_FILTER = FILTER value
  • AF_non_cancer_popmax max value of: 
    AF_non_cancer_afr
AF_non_cancer_amr
AF_non_cancer_eas
AF_non_cancer_nfe
AF_non_cancer_sas
    when available
  • AF_non_cancer_all_popmax get max value of bottleneck populations: 
    AF_non_cancer_ami
AF_non_cancer_asj
AF_non_cancer_fin
AF_non_cancer_mid
AF_non_cancer_oth
    and set to the greater of calculated AF_non_cancer_popmax or max of bottleneck populations. Example command: Installed python package pysam==0.22.0, used the same chr list and ran:
cat chr_list.txt | xargs -IFN -P 8 python3 custom_vcf_info.py --input_vcf gnomad.genomes.v3.1.1.sites.FN.bcftools_INFO_subset.vt_norm.vcf.gz --output_basename gnomad.genomes.v3.1.1.sites.FN.custom --threads 2

Create echtvar reference

Used docker image pgc-images.sbgenomics.com/d3b-bixu/echtvar:0.1.9 First, create a config JSON file. See here for generic details. This config was used. This config will prepend gnomad_3_1_1_ to all field names for source clarity upon annotation.

echtvar \
   encode \
   gnomad.v3.1.1.custom.echtvar.zip \
   gnomad_update.json \
   *.custom.INFO_added.vcf.gz