update clinvar script
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=20170130
+DATE=20181028
+fasta=/data/human/g1k_v37_decoy.fa
-wget -O cv.vcf.gz ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive/2017/clinvar_${DATE}.vcf.gz
+
+wget -O cv.vcf.gz ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2018/clinvar_${DATE}.vcf.gz
vt decompose -s cv.vcf.gz \
| python clinvar.py \
- | vt normalize -r /data/human/human_g1k_v37.fasta - \
+ | vt normalize -r $fasta - \
| bgzip -c > clinvar_$DATE.tidy.vcf.gz
tabix clinvar_$DATE.tidy.vcf.gz

update clinvar script