Importing Varscan Vcf To Igv
2
1
Entering edit mode
11.7 years ago
jackuser1979 ▴ 890

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
vcf igv • 4.8k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
11.7 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
Entering edit mode
11.7 years ago

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1407 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6