Added a fix to make-gnomad.sh perl regex to avoid removing AF column from INFO field of multi-allelic sites in gnomad exomes vcf
MODIFY
gemini/annotation_provenance/make-gnomad.sh
gemini/annotation_provenance/make-gnomad.sh
wget -O - https://data.broadinstitute.org/gnomAD/release-170228/exomes/vcf/gnomad.exomes.r2.0.1.sites.vcf.gz | zcat - | perl -pe 's/;CSQ.+//g' | less | bgzip -c > gnomad.exomes.r2.0.1.sites.no-VEP.vcf.gz
zcat gnomad.exomes.r2.0.1.sites.no-VEP.vcf.gz \
- | perl -pe 's/(;[^_\s]+_HIST(_AL[LT])?=[^;]+)//g' \
+ | perl -pe 's/(;[^_\s;]+_HIST(_AL[LT])?=[^;]+)//g' \
| vt decompose -s - \
| vt normalize -r ~/bcbio/genomes/Hsapiens/g1k_v37_decoy/seq/g1k_v37_decoy.fa - \
| bgzip -c > gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz

Added a fix to make-gnomad.sh perl regex to avoid removing AF column from INFO field of multi-allelic sites in gnomad exomes vcf