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

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
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updated by Ram Ram • written by bingnas • bingnas

1 answer

WT=1 0/0

HET=1 0/1

HOM=1 1/1

NC=1 .

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updated by Ram Ram • written by michael.d.mclellan michael.d.mclellan

Thank you so much Michael

• 1 views • link
written by bingnas • bingnas

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

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written by bingnas • bingnas

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