Question: Beagle: Skip intervals with no common markers
gravatar for NS
12 months ago by
NS10 wrote:

Hi I am using Beagle to perform genotype imputation. I first used conform-gt to adjust genomic position, allele order and chr strand of the markers in my vcf.gz data to match the reference panel. Then I ran this command with Beagle to perform imputation per chromosome:

 java -Xmx50g -jar beagle.25Nov19.28d.jar gt=chr1.vcf.gz out=imputed_b37_imputed ref=chr1.1kg.phase3.v5a.b37.bref3 chrom=1 impute=true

After several hours of running, I get the following error:

ERROR: Reference and target files have no markers in common in interval: 

Common markers must have identical CHROM, POS, REF, and ALT fields.
Exiting program.

How can I skip the intervals with no common markers and proceed with imputation, without exiting the program ?

beagle plink conformgt vcf • 515 views
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