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 can'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
