Closed liserjrqlxue closed 2 years ago
Hi, thanks for the complete description. Yes, the VCF insertion is treated as (in BED 0-based half-open):
1 874777 874778
and the bed interval is:
1 874778 874888
these do not overlap! So no parameter change will allow these to overlap. You could, instead, expand your bed regions by $n bases.
If you have encountered an error, please include:
line 2 is the real Simple Tandem Repeat Information tag I want to annotated.
get from
tabix -h https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz 1:874778-874778 |bgzip > test.vcf.gz
There're deletion or duplication of seqCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA
at 1:874779-874826============================================= vcfanno version 0.3.2 [built with go1.14.4]
see: https://github.com/brentp/vcfanno
vcfanno.go:115: found 1 sources from 1 files vcfanno.go:156: falling back to non-bgzip vcfanno.go:248: annotated 3 variants in 0.00 seconds (1962.4 / second)
1 874778 1164669 G GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA . . ALLELEID=1153717;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817_874864dup;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=Duplication;CLNVCSO=SO:1000035;CLNVI=Invitae:1613992;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;repeat=trf-1 1 874778 1108252 G GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA . . ALLELEID=1089348;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817CCCCTCATCACCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATC[3];CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;CLNVC=Microsatellite;CLNVCSO=SO:0000289;CLNVI=Invitae:3807250;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;repeat=trf-1 1 874778 769497 GCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA G . . ALLELEID=777163;CLNDISDB=MedGen:CN517202;CLNDN=not_provided;CLNHGVS=NC_000001.10:g.874817_874864del;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=Deletion;CLNVCSO=SO:0000159;CLNVI=Invitae:1680099;GENEINFO=SAMD11:148398;MC=SO:0001575|splice_donor_variant;ORIGIN=1;RS=568340123;repeat=trf-1,trf;left_repeat=trf-1;right_repeat=trf-1,trf