Transform txt files with SNPs from ForenSeq kit to proper format for plink
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16 months ago
dzisis1986 ▴ 70

Hello I have .csv files for different samples with the following information

Locus   Genotype    QC Indicators
rs6690515   G,G 
rs28635343  C,C 
rs16824588  T,C 
rs424079    A,A 

and

Locus   Allele_Name Typed_Allele?   Reads
  rs6690515 A   No  0
  rs6690515 G   Yes 392
  rs28635343    C   Yes 4001
  rs28635343    T   No  0
  rs16824588    C   Yes 595
  rs16824588    T   Yes 486
  rs424079  A   Yes 1051
  rs424079  C   No  0

Is it possible to manipulate and change this information in order to create proper file format for Plink ? Can I create .ped or .map files from that ?

plink python SNPs • 324 views
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