Importing Varscan Vcf To Igv

Question

[jackuser1979]

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

[Pierre Lindenbaum]

can you show us the first lines of the VCF...

Answer 1

[Pierre Lindenbaum]

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

[jackuser1979]

It is alignment problem when I copy pasted few lines to this forum. There is no alignment problem in my original file.

[Istvan Albert]

double check, if it pastes in a funny way it means that your original file only looks right but it is not

Answer 2

[Sean Davis]

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

[jackuser1979]

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