Eagle phasing and minimac imputation
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4.8 years ago
dp0b ▴ 70

Hi,

I wish to use eagle phasing and minimac imputation to impute to whole genome sequence.

I have successfully phased my genotypes using eagle but Im struggling to read them into minimac. Minimac will tell me there are no marker overlaps between the target and reference, when there definitely is. Can minimac read in eagle phased files directly?

My original files for phasing with eagle were plink binary files and when I specify vcf format for minimac they read in but then I get the no overlap error I was hoping someone could help me with the input line; I have tried the following;

./minimac --vcfReference --refHaps phased_seq.haps --haps impute_ani_phased.haps --snps target.snps --rs --rounds 5 --states 200 --prefix minimac_imputed

./minimac --vcfReference --refHaps phased_seq.haps --shape_haps impute_ani_phased.haps --chr 29 --sample impute_ani_phased.sample --rs --rounds 5 --states 200 --prefix minimac_imputed

the target snps was a file in the format

29:100
29:2000

and my phased files were in the format

29 29:16860 16860 A G 1 1 1 1
29 29:168604 168604 G A 1 1 0 1
29 29:168680 16860369 G A 1 1 1 1

Many thanks

eagle minimac imputation phasing genotypes • 2.4k views
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