Hi,
I have .vcf file , which i am passing to IGV standalone tool to convert it to idx file. While doing so the igv tool gives me the followign error
"There are too many keys for the sample XXXXX Keys Gene Description=XXXX;OMIM ID=xxxx;Gene Description=xxxx; OMIM ID=xxxx....................................................."
In vcf file , i could see in the info field there are multiple entries for Gene Description and OMIM ID keys
e.g.:
DP=2167;VDB=0.0023;AF1=1;AC1=2;DP4=0,0,1112,1019;MQ=44;FQ=-282;EFF=INTRON(MODIFIER||||CASQ2|mRNA|CODING|NM_001232|);pValue=9.999999999999999E-223;PUBMED_CITATIONS=0;GLOBAL_MAF=0.3480;HGVS=NC_000001.10:g.116260532A>T,NM_001232.3:c.784-17T>A,;pValue=9.999999999999999E-223;Category=2 Gene Description=116311162;OMIM ID=omimMorbid:114251; Gene Description=116311162;OMIM ID=omimMorbid:114251;TYPE=SNP;Zygosity=HOM GT:PL:GQ
Kindly let me know what is to be done...
Is there anything wrong with the vcf?
I have .vcf file , which i am passing to IGV standalone tool to convert it to idx file. While doing so the igv tool gives me the followign error
"There are too many keys for the sample XXXXX Keys Gene Description=XXXX;OMIM ID=xxxx;Gene Description=xxxx; OMIM ID=xxxx....................................................."
In vcf file , i could see in the info field there are multiple entries for Gene Description and OMIM ID keys
e.g.:
DP=2167;VDB=0.0023;AF1=1;AC1=2;DP4=0,0,1112,1019;MQ=44;FQ=-282;EFF=INTRON(MODIFIER||||CASQ2|mRNA|CODING|NM_001232|);pValue=9.999999999999999E-223;PUBMED_CITATIONS=0;GLOBAL_MAF=0.3480;HGVS=NC_000001.10:g.116260532A>T,NM_001232.3:c.784-17T>A,;pValue=9.999999999999999E-223;Category=2 Gene Description=116311162;OMIM ID=omimMorbid:114251; Gene Description=116311162;OMIM ID=omimMorbid:114251;TYPE=SNP;Zygosity=HOM GT:PL:GQ
Kindly let me know what is to be done...
Is there anything wrong with the vcf?