Hi
I am working with 1000 Genomes Phase 3 data VCF files( Completely Phased and Genotyped). I want to Calculate EHH and IHH scores for this data for which I am using REHH 2.0 package of R. I filtered the VCF files using VCFtools, SNPs_only option, Extracted haplotypes from VCF file containing phased genotypes and applied vcftools with --IMPUTE option to create .hap files. Using Custom script I created .inp(map) files which has a list of SNPs with positions and chromosome IDs
Now I am running the command data2haplohh in rehh package of R.
chr3aa<-data2haplohh(hap_file="chr3hapaa.hap", map_file="chr3mapaa.inp", recode.allele=TRUE, haplotype.in.columns=TRUE)
The error I am getting is:
Map file seems OK: 15000 SNPs declared for chromosome 3
Haplotype are in columns with no header
Alleles are being recoded according to map file as: 0 (missing data), 1 (ancestral allele) or 2 (derived allele)
Discard Haplotype with less than 100 % of genotyped SNPs
5008 Haplos discarded 0 Haplos remaining
Error in data2haplohh(hap_file = "chr3hapaa.hap", map_file = "chr3mapaa.inp", : No haplotype left after filtering of missing data: check allele coding (e.g., correspondance of allele coding between the map_inp and haplotype input file) data or relax the value of min_perc_geno.hap to allow for more missing data
Any help or suggestions will be appreciated. Thanks
