Question: Importing Varscan Vcf To Igv
1
gravatar for jackuser1979
6.5 years ago by
jackuser1979860
US
jackuser1979860 wrote:

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".

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
vcf bioinformatics igv • 3.1k views
ADD COMMENTlink modified 6.5 years ago by Sean Davis25k • written 6.5 years ago by jackuser1979860

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

ADD REPLYlink written 6.5 years ago by Pierre Lindenbaum117k
2
gravatar for Pierre Lindenbaum
6.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum117k wrote:

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

ADD COMMENTlink written 6.5 years ago by Pierre Lindenbaum117k

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

ADD REPLYlink written 6.5 years ago by jackuser1979860

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

ADD REPLYlink written 6.5 years ago by Istvan Albert ♦♦ 79k
2
gravatar for Sean Davis
6.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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

ADD COMMENTlink written 6.5 years ago by Sean Davis25k

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

ADD REPLYlink written 6.5 years ago by jackuser1979860
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