Did any one tried importing varscan variant caller ( V.2.3.2) VCF output to IGV (V 2.1.2.4)?. I tried indexing VCF file using igvtools-index & Tabix command. It says error Error for input string:"PASS.
A few lines of my VCF format:
##fileformat=VCFv4.0
##source=VarScan2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##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
gi|671553188|gb|JH556661.1| 2200443 . G A PASS DP=21 GT:GQ:DP 0/1:1:21
gi|671553188|gb|JH556661.1| 2594155 . C A PASS DP=24 GT:GQ:DP 0/1:3:24
gi|671553188|gb|JH556661.1| 2594175 . C A PASS DP=26 GT:GQ:DP 0/1:4:26
gi|671553188|gb|JH556661.1| 2594192 . A G PASS DP=25 GT:GQ:DP 0/1:3:25
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jackuser1979
There is a space before "#CHROM"
a tab is missing between "POS" and "ID"
the QUAL column is missing in the body of the VCF ile
It is alignment problem when I copy pasted few lines to this forum. There is no alignment problem in my original file.
double check, if it pastes in a funny way it means that your original file only looks right but it is not
At least with versions of VarScan that we have used, the VCF files are broken. We use this code to fix them up:
https://bitbucket.org/meltzerlab/seqtools/src/505952611251/seqtools/varscan.py
Thanks for the code. I have already have VCF file. But this code parse output from varscan. When I run the script, it shows error :python varscan.py myfile.vcf>myfilefix.vcf usage: Parse VCF output from Varscan to output valid VCF. Output is to stdout. [-h] [-v VARSCAN] Parse VCF output from Varscan to output valid VCF. Output is to stdout.: error: unrecognized arguments: myfile.vcf
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can you show us the first lines of the VCF...