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 map=plink.chr1.GRCh37.map 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: 1:165113264-205459274 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 ?