update to dbsnp 151. see
MODIFY
gemini/annotation_provenance/make-dbsnp.sh
gemini/annotation_provenance/make-dbsnp.sh
@@ -36,6 +36,6 @@ fields=$(bcftools view -h $f | grep INFO | grep -Po "ID=[^,]+" | awk '{ print "I
bcftools annotate -x $fields $f --threads 3 \
| vt decompose -s - \
| vt normalize -r /data/human/g1k_v37_decoy.fa - \
- | bcftools annotate -x INFO/OLD_MULTIALLELIC -O z -o dbsnp.$v.$date.tidy.vcf.gz \
+ | bcftools annotate -x INFO/OLD_MULTIALLELIC,INFO/OLD_VARIANT -O z -o dbsnp.$v.$date.tidy.vcf.gz \
&& tabix dbsnp.$v.$date.tidy.vcf.gz

MODIFY
gemini/annotations.py
gemini/annotations.py
@@ -25,7 +25,7 @@ def get_anno_files(args):
annos = {
'pfam_domain': os.path.join(anno_dirname, 'hg19.pfam.ucscgenes.bed.gz'),
'cytoband': os.path.join(anno_dirname, 'hg19.cytoband.bed.gz'),
- 'dbsnp': os.path.join(anno_dirname, 'dbsnp.b147.20160601.tidy.vcf.gz'),
+ 'dbsnp': os.path.join(anno_dirname, 'dbsnp.151.20180423.tidy.vcf.gz'),
'clinvar': os.path.join(anno_dirname, 'clinvar_20190102.tidy.vcf.gz'),
'gwas': os.path.join(anno_dirname, 'hg19.gwas.bed.gz'),
'rmsk': os.path.join(anno_dirname, 'hg19.rmsk.bed.gz'),

MODIFY
gemini/install-data.py
gemini/install-data.py
@@ -19,7 +19,7 @@ The recommended Gemini install location is /usr/local/share/gemini.
anno_files = \
['hg19_fitcons_fc-i6-0_V1-01.bed.gz',
-'dbsnp.b147.20160601.tidy.vcf.gz',
+'dbsnp.151.20180423.tidy.vcf.gz',
'clinvar_20190102.tidy.vcf.gz',
'29way_pi_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.hg19.merged.bed.gz',
'hg19.CpG.bed.gz',
@@ -64,7 +64,6 @@ toadd_anno_files = []
anno_versions = {
"ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz": 4,
"GRCh37-gms-mappability.vcf.gz": 2,
- "dbsnp.b147.20160601.tidy.vcf.gz": 1,
"hg19.rmsk.bed.gz": 2,
"detailed_gene_table_v75": 2,
"summary_gene_table_v75": 2,

update to dbsnp 151. see #912