Question: How to prepare myfile.hlist for haplotype analyses in PLINK
gravatar for arrow641
6.4 years ago by
United States
arrow64110 wrote:

Hi Everybody,

     When I prepare the specific haplotype file (haplotype_31.hlist ), a problem happen. PLINK remind me file error as below, I don’t know which haplotype should be imputed in column 7 and column8+? I hope to get 2/3/4 SNPs haplotypes within 31 SNPs, I have 2145 participants. could you help me? I try Sliding window specification, but it cann't cross different chromosome. 

 Thank you very much.

Plink command and file description is below:

plink --file mydata --hap myfile.hlist

will read the file myfile.hlist, each row of which is expected to have one of the three following formats:

1) Particular allele specified

The first format specifies a particular haplotype at a given locus. Two example rows of this format are:

     rs1001 5 0 201  1 2   TC    snp1 snp2
     rs1002 5 0 202  A C   TTA   snp1 snp3 snp4

The columns represent:

     Col 1  : Imputed SNP name
     Col 2  : Imputed SNP chromosome
     Col 3  : Imputed SNP genetic distance (default: Morgan coding)
     Col 4  : Imputed SNP physical position (bp units)
     Col 5  : Imputed SNP allele 1 name
     Col 6  : Imputed SNP allele 2 name
     Col 7  : Tag SNP allele/haplotype that equals imputed SNP allele 1
     Col 8+ : Tag SNP(s) [in same order as haplotype in Col 7]
  2) my file is as below:

Col 1     col2     col3          col4           col5      col6        col7     col8

rs1334000  1          0          71806840        A          C          AC        CC

rs3795698  1          0          71831344        T          G          TG        TT

rs10493485 1          0          71843717        T          A          TA        AT


3) PLINK error reminder:

ERROR:Problem with Haplotype_31.hlist line

rs1334000   1          0          71806840        A          C          AC        CC

plink haplotype hlist • 3.9k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 6.4 years ago by arrow64110
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