How to Convert SNP's that produced from Varscan into 0,1,2 ?

Question

[bingnas]

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

[Veera]

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.

[bingnas]

Yes, it came from VarScan package

[Chirag Nepal]

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

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