Question: How to Convert SNP's that produced from Varscan into 0,1,2 ?
0
gravatar for bingnas
4.1 years ago by
bingnas10
United States
bingnas10 wrote:

hello everyone

I have snp's data from VarScan like 

#CHROM     POS   ID     REF    ALT    QUAL    FILTER    INFO    FORMAT    Sample1
    chr1       12198    .      G        C          .           PASS    ADP=54;WT=0;HET=1;HOM=0;NC=0    
    chr1       12783    .      G        A          .           PASS    ADP=58;WT=0;HET=1;HOM=0;NC=0   
    chr1       13116    .      T        G          .           PASS    ADP=30;WT=0;HET=1;HOM=0;NC=0  

could you please help me to convert the SNP's to 0,1,2?

Thank you so much in advance 

Elme

snp • 1.1k views
ADD COMMENTlink modified 4.0 years ago • written 4.1 years ago by bingnas10

What do you mean by "convert to 0,1,2" ?

Instead, you can output the varscan file in .vcf format.

ADD REPLYlink written 4.0 years ago by Chirag Nepal2.2k
0
gravatar for Veera
4.1 years ago by
Veera 90
Denmark
Veera 90 wrote:

Is it a VCF file ? Then you can read the VCF file and convert it to any format you want. But you need to specify what software you are planning to use, so that you'll get useful answers.

 

 

 

 

 

 

ADD COMMENTlink written 4.1 years ago by Veera 90
0
gravatar for bingnas
4.0 years ago by
bingnas10
United States
bingnas10 wrote:

Yes, it came from VarScan package 

ADD COMMENTlink written 4.0 years ago by bingnas10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2862 users visited in the last hour