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


snp • 1.2k views
ADD COMMENTlink modified 3.9 years ago by Biostar ♦♦ 20 • written 4.9 years ago by bingnas10
gravatar for michael.d.mclellan
4.8 years ago by
United States
michael.d.mclellan150 wrote:

WT=1 0/0

HET=1 0/1

HOM=1 1/1

NC=1 .

ADD COMMENTlink written 4.8 years ago by michael.d.mclellan150

Thank you so much Michael

ADD REPLYlink written 4.8 years ago by bingnas10

can you more explain please! 0/0 mean homo and 1/1 also homo (dominant and recessive )?

and 0/1 is hero? . is missing?

Thank you Elme

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by bingnas10
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