error when imputing for mismatch legend file
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3 months ago
raalsuwaidi ▴ 10

hi all,

i am facing the following error using IMPUTE2

ERROR: The number of haplotypes (-h) files must match the number of legend (-l) files on the command line.

so i created the legend file using the same haps file as per below

shapeit -convert --input-haps merged_shapeit.QC.CHR1.vcf.haps merged_shapeit.QC.CHR1.vcf.sample --output-ref merged_shapeit.QC.CHR1.vcf.hap merged_shapeit.QC.CHR1.vcf.leg merged_shapeit.QC.CHR1.vcf.sam

but i am still getting the same error when i run the impute code below

impute2 -m /home/reem/impute/data/geneticmap/genetic_map_b36/genetic_map_chr1_b36.txt -known_haps_g /bmshare/reem/shapeit/minorAllelemerged_shapeit.QC.CHR1-AF.vcf.haps -int 20.4e6 20.5e6 -Ne 20000 -h /bmshare/reem/shapeit/merged_shapeit.QC.CHR1.vcf.haps / -l /bmshare/reem/shapeit/merged_shapeit.QC.CHR1.vcf.leg -o /bmshare/reem/WGS/results/minorAllelemerged_shapeit.QC.CHR1-AF.vcf

any insight?

impute2 haps shapeit legend • 131 views
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