How can I create genetic map for impute2 using vcf files containing SNPs?
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28 days ago
Sakib • 0

I am new to bioinformatics and am trying to perform imputation on a plant dataset. First, I aligned reads to the reference genome and then performed SNP calling. I chose samples with higher coverage to create a reference panel. Now, I am trying to perform imputation using impute2 and Beagle. I ran the beagle with the available vcf files and it is running. I am stuck with impute2. It requires a genetic map to perform the imputation. I tried creating a genetic map with

vcftools --gzvcf {input.vcf} --plink --out data/impute2/genetic_map

The output looked like

1       chr1:651        0       651

When I ran impute2 I got the error

-reading genetic map from -m file 
--filename=[data/impute2/genetic_map/genetic_map.txt]
ERROR: The genetic map file [data/impute2/genetic_map/genetic_map.txt] does not conform to the required three-column format. Please review the online documentation and try again.

I am not sure how I can create the genetic map. Apart from the aligned reads (.bam) and snps (.vcf) file I don't have any other information.

I would really appreciate any help that anyone can provide.

imputation vcftools snps plink impute2 • 199 views
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