update gnomad to 2.0.2 and decompose with new vt
closes
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 \
+wget -O - https://storage.googleapis.com/gnomad-public/release/2.0.2/vcf/exomes/gnomad.exomes.r2.0.2.sites.vcf.bgz \
+ | zcat - \
+ | perl -pe 's/;CSQ.+//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
+ | ~/src/vt/vt decompose -s - \
+ | ~/src/vt/vt normalize -r /data/human/g1k_v37_decoy.fa - \
+ | bgzip -c > gnomad.exomes.r2.0.2.sites.no-VEP.nohist.tidy.vcf.gz
-tabix -f gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz
+tabix -f gnomad.exomes.r2.0.2.sites.no-VEP.nohist.tidy.vcf.gz

MODIFY
gemini/annotations.py
gemini/annotations.py
@@ -53,7 +53,7 @@ def get_anno_files(args):
'fitcons': os.path.join(anno_dirname, "hg19_fitcons_fc-i6-0_V1-01.bed.gz"),
'cosmic': os.path.join(anno_dirname, 'cosmic-v68-GRCh37.tidy.vcf.gz'),
'exac': os.path.join(anno_dirname, 'ExAC.r0.3.sites.vep.tidy.vcf.gz'),
- 'gnomad': os.path.join(anno_dirname, 'gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz'),
+ 'gnomad': os.path.join(anno_dirname, 'gnomad.exomes.r2.0.2.sites.no-VEP.nohist.tidy.vcf.gz'),
'geno2mp': os.path.join(anno_dirname, 'geno2mp.variants.tidy.vcf.gz'),
}
# optional annotations

MODIFY
gemini/install-data.py
gemini/install-data.py
@@ -52,7 +52,7 @@ anno_files = \
'summary_gene_table_v75',
'cancer_gene_census.20140120.tsv',
'ExAC.r0.3.sites.vep.tidy.vcf.gz',
-'gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz',
+'gnomad.exomes.r2.0.2.sites.no-VEP.nohist.tidy.vcf.gz',
'geno2mp.variants.tidy.vcf.gz',
]
extra_anno_files = {"gerp_bp": "hg19.gerp.bw", "cadd_score": "whole_genome_SNVs.tsv.compressed.gz"}
@@ -73,7 +73,7 @@ anno_versions = {
"ESP6500SI.all.snps_indels.tidy.v2.vcf.gz": 2,
'ExAC.r0.3.sites.vep.tidy.vcf.gz': 4,
'geno2mp.variants.tidy.vcf.gz': 1,
- 'gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz': 2,
+ 'gnomad.exomes.r2.0.2.sites.no-VEP.nohist.tidy.vcf.gz': 1,
"whole_genome_SNVs.tsv.compressed.gz": 2,
}

update gnomad to 2.0.2 and decompose with new vt

closes #895