update clinvar.
MODIFY
docs/content/history.rst
docs/content/history.rst
@@ -18,6 +18,7 @@ Release History
#. Fix browser query report (thanks @Nmael see #818).
#. Allow specifying a --where clause for `gene_wise` to filter considered variants. (Thanks Uma for suggestion).
#. Fix bug in propagating vep-extras to variant_impacts table (Thanks Sergey for reporting).
+#. Update clinvar annotation.
0.19.1
======

MODIFY
gemini/annotation_provenance/make-clinvar.sh
gemini/annotation_provenance/make-clinvar.sh
#wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20150305.vcf.gz \
#tabix clinvar_20150305.vcf.gz
-DATE=20160203
+DATE=20170130
-wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_$DATE.vcf.gz \
+wget -O cv.vcf.gz ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive/2017/clinvar_${DATE}.vcf.gz
-vt decompose -s clinvar_$DATE.vcf.gz \
+vt decompose -s cv.vcf.gz \
| python clinvar.py \
- | vt normalize -r /data/human/b37/human_g1k_v37_decoy.fasta - \
+ | vt normalize -r /data/human/human_g1k_v37.fasta - \
| bgzip -c > clinvar_$DATE.tidy.vcf.gz
tabix clinvar_$DATE.tidy.vcf.gz

MODIFY
gemini/annotations.py
gemini/annotations.py
@@ -25,7 +25,7 @@ def get_anno_files(args):
'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'),
- 'clinvar': os.path.join(anno_dirname, 'clinvar_20160203.tidy.vcf.gz'),
+ 'clinvar': os.path.join(anno_dirname, 'clinvar_20170130.tidy.vcf.gz'),
'gwas': os.path.join(anno_dirname, 'hg19.gwas.bed.gz'),
'rmsk': os.path.join(anno_dirname, 'hg19.rmsk.bed.gz'),
'segdup': os.path.join(anno_dirname, 'hg19.segdup.bed.gz'),

MODIFY
gemini/install-data.py
gemini/install-data.py
@@ -20,7 +20,7 @@ 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',
-'clinvar_20160203.tidy.vcf.gz',
+'clinvar_20170130.tidy.vcf.gz',
'29way_pi_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.hg19.merged.bed.gz',
'hg19.CpG.bed.gz',
'hg19.pfam.ucscgenes.bed.gz',
@@ -65,7 +65,7 @@ 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,
- "clinvar_20160203.tidy.vcf.gz": 5,
+ "clinvar_20170130.tidy.vcf.gz": 5,
"hg19.rmsk.bed.gz": 2,
"detailed_gene_table_v75": 2,
"summary_gene_table_v75": 2,

MODIFY
test/test-clinvar.sh
test/test-clinvar.sh
@@ -10,14 +10,14 @@ export -f check
####################################################################
# 1. Test clinvar annotations
####################################################################
-echo " clinvar.t01...\c"
-echo "chr1 985955 1 pathogenic Myasthenic_syndrome,_congenital,_with_pre-_and_postsynaptic_defects OMIM_Allelic_Variant 103320.0001 germline MedGen:OMIM:Orphanet C3808739:615120:ORPHA590 RCV000019902.29 1 0 C
+echo " clinvar.t01..."
+echo "chr1 985955 1 pathogenic Myasthenic_syndrome,_congenital,_8|Congenital_myasthenic_syndrome OMIM_Allelic_Variant 103320.0001 germline MedGen:OMIM|MedGen:Orphanet C3808739:615120|C0751882:ORPHA590 RCV000019902.30|RCV000235029.1 1 0 C
chr1 1199489 0 None None None None None None None None 0 0 None
-chr1 1959699 1 other Generalized_epilepsy_with_febrile_seizures_plus_type_5|Epilepsy,_juvenile_myoclonic_7|Epilepsy,_idiopathic_generalized_10 OMIM_Allelic_Variant 137163.0002 germline MedGen|MedGen|MedGen:OMIM C3150401|CN043549|C2751603:613060 RCV000017599.2|RCV000017600.2|RCV000022558.2 1 0 A
-chr1 161276553 1 pathogenic Roussy-Levy_syndrome|Charcot-Marie-Tooth_disease_type_1B OMIM_Allelic_Variant 159440.0021 germline MedGen:OMIM:SNOMED_CT|GeneReviews:MedGen:OMIM:Orphanet:SNOMED_CT C0205713:180800:45853006|NBK1205:C0270912:118200:ORPHA101082:42986003 RCV000015250.25|RCV000192587.1 1 0 T
+chr1 1959699 1 other Generalized_epilepsy_with_febrile_seizures_plus_type_5|Epilepsy,_juvenile_myoclonic_7|Epilepsy,_idiopathic_generalized_10 OMIM_Allelic_Variant|UniProtKB_(protein) 137163.0002|O14764#VAR_043153 germline MedGen|MedGen|MedGen:OMIM C3150401|C2751604|C2751603:613060 RCV000017599.2|RCV000017600.2|RCV000022558.2 1 0 A
+chr1 161276553 1 pathogenic Roussy-Levy_syndrome|Charcot-Marie-Tooth_disease,_demyelinating,_type_1b OMIM_Allelic_Variant|UniProtKB_(protein) 159440.0021|P25189#VAR_015978 germline MedGen:OMIM:Orphanet:SNOMED_CT|MedGen:OMIM:Orphanet:SNOMED_CT C0205713:180800:ORPHA3115:45853006|C0270912:118200:ORPHA101082:42986003 RCV000015250.26|RCV000192587.1 1 0 T
chr1 235891431 0 None None None None None None None None 0 0 None
chr1 247587093 1 not-provided Familial_cold_urticaria . . unknown MedGen:OMIM:Orphanet:SNOMED_CT C0343068:120100:ORPHA47045:238687000 RCV000084222.1 1 0 T
-chr3 33063141 1 not-provided Juvenile_GM>1<_gangliosidosis . . somatic MedGen:OMIM:Orphanet:Orphanet:SNOMED_CT C0268272:230600:ORPHA354:ORPHA79256:18756002 RCV000056404.1 1 0 A
+chr3 33063141 1 not-provided GM1_gangliosidosis_type_2 . . somatic MedGen:OMIM:Orphanet:SNOMED_CT C0268272:230600:ORPHA79256:18756002 RCV000056404.1 1 0 A
chrX 31200832 0 benign not_specified . . germline MedGen CN169374 RCV000080867.3 0 0 AT
chrX 89963314 0 None None None None None None None None 0 0 None" > exp
@@ -36,8 +36,9 @@ gemini query -q "select chrom, end, in_omim,
check obs exp
rm obs exp
-echo " clinvar.t02\c"
-echo "B3GALT6 ehlers-danlos_syndrome\x2c_progeroid_type\x2c_2|spondyloepimetaphyseal_dysplasia_with_joint_laxity\x2c_type_1\x2c_with_fractures|spondyloepimetaphyseal_dysplasia_with_joint_laxity
+echo " clinvar.t02..."
+echo "B3GALT6 ehlers-danlos_syndrome\x2c_progeroid_type\x2c_2|spondyloepimetaphyseal_dysplasia_with_joint_laxity|spondyloepimetaphyseal_dysplasia_with_joint_laxity\x2c_type_1\x2c_with_fractures
SCNN1D None" > exp
+
gemini query -q "select gene, clinvar_gene_phenotype from variants" test.clinvar_gene_pheno.db > obs
check obs exp

update clinvar.