Question: Error while running R package rehh
gravatar for shrutishreyajha
3.0 years ago by
shrutishreyajha0 wrote:


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,

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

snp rehh R • 1.2k views
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