CLC Genomics workbench and dbSNP VCF import
I have tried to import a dbSNV vcf file into my workbench's reference genome, but error like that occurred and i am now, not able to make dbSNV track. The error :
Time Elapsed time Description
Sat Aug 10 21:21:47 GMT+09:00 2024 0:00:00 Skipped line 7 of C:\Users\myname\OneDrive - affilication name \2024myfile\Dry\reference\intersection_10001.vcf: Input is not VCF format compliant: Missing required header line.
The VCF file I tried to import is like this:
##fileformat=VCFv4.1
##FILTER=<ID=q25,Description="Quality below 25">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1
1 135 . C T 28 PASS DP=5 GT:GQ:DP 1|1:28:5
1 138 . T C 36 PASS DP=5 GT:GQ:DP 1|1:36:5
1 346 . C T 32 PASS DP=3 GT:GQ:DP 1|1:32:3
Could you please help me with solving this issue?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Count and filter sites with degenarate bases in VCF files
written by ja569116 •
-
vcf file
written by karthick •
-
vcf problem removing MAXGT and POLY
written by karthick •
-
How do I subset VCF based on genotype?
written by Tine •
-
Filter vaiants having no AF information
written by waqaskhokhar999
-
Get genotype GT from multi-sample VCF (per chromosome)
written by zx8754
-
Calculating Variant Allele Frequency
written by novice
-
summarize SNPs and indels information in vcf file
written by Kurban
-
Variant Effect Predictor On Domain Level
written by jackuser1979
-
Importing Varscan Vcf To Igv
written by jackuser1979
Since you are paying for a CLC license it may be easiest to work with their tech support. You can also share the data directly with them to see what is going wrong.