Smaller gnomAD 3.1.2 VCF

gnomad_vcf_prep.txt

# Fetch the WGS gnomAD 3.1.2 per-chrom VCFs (the large size is mostly due to INFO fields):
mkdir gnomad
gsutil -m cp gs://gcp-public-data--gnomad/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chr*.vcf.bgz gnomad
gsutil -m cp gs://gcp-public-data--gnomad/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chr*.vcf.bgz.tbi gnomad

# Shortlist INFO fields we want to keep when merging these into a single VCF of reduced file size:
bcftools view -h gnomad/gnomad.genomes.v3.1.2.sites.chr21.vcf.bgz | grep ^##INFO | cut -f3- -d= |  grep -Ev "controls|non_cancer|non_neuro|non_topmed|non_v2|vep" | sort | less -S

cadd_phred
cadd_raw_score
primate_ai_score
revel_score
splice_ai_consequence
splice_ai_max_ds

# Make a merged 3.1.2 VCF listing only the shortlisted INFO fields:
ls gnomad/gnomad.genomes.v3.1.2.sites.chr*.vcf.bgz | xargs bcftools concat --threads 16 -n | bcftools annotate --threads 16 --remove ^INF/AC,INF/AN,INF/AF,INF/AC_raw,INF/nhomalt,INF/popmax,INF/AC_popmax,INF/nhomalt_popmax,INF/MQ,INF/cadd_phred,INF/cadd_raw_score,INF/primate_ai_score,INF/revel_score,INF/splice_ai_consequence,INF/splice_ai_max_ds --output-type z --output gnomad/gnomad.genomes.v3.1.2.sites.vcf.bgz
tabix -p vcf gnomad/gnomad.genomes.v3.1.2.sites.vcf.bgz