Question: How to Convert SNP's that produced from Varscan into 0,1,2 ?
gravatar for bingnas
3.6 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 • 918 views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 3.6 years ago by bingnas10
gravatar for michael.d.mclellan
3.5 years ago by
United States
michael.d.mclellan140 wrote:

WT=1 0/0

HET=1 0/1

HOM=1 1/1

NC=1 .

ADD COMMENTlink written 3.5 years ago by michael.d.mclellan140

Thank you so much Michael

ADD REPLYlink written 3.5 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 2.6 years ago • written 2.6 years ago by bingnas10
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