update history and install-data for newest gnomad
MODIFY
docs/content/history.rst
docs/content/history.rst
@@ -11,6 +11,7 @@ Release History
#. Allow `--gt-filter` to specify the gt_type, e.g. `(gt_quals).(=HET).(<20).(all)` (thanks Jessica for suggesting)
#. Add `--gene-where` argument to `comp_hets` tool to dictate how variants are restricted to genes. (thanks Jessica for suggesting)
#. genewise: don't show any variants that don't meet the required number of optional filters.
+#. Fix AF for decomposed gnomad variants (thanks @mbootwalla).
0.20.0
======

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
-tabix -f gnomad.exomes.r2.0.1.sites.no-VEP.nohist.vcf.gz
+tabix -f gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz

MODIFY
gemini/install-data.py
gemini/install-data.py
@@ -73,6 +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,
"whole_genome_SNVs.tsv.compressed.gz": 2,
}

update history and install-data for newest gnomad