I am a novice in the world of bioinformatics. I am attempting to work out genotype imputation for a set of 8K+ samples. I am only interested in imputing data for chromosome 6 to be used in later downstream analysis. I am using Beagle for the genotype imputation using the following script:
java -Xss5m -Xmx16g \ -jar beagle.18May20.d20.jar \ gt=immuno_chrom6_for_imputation.vcf.gz \ ref=chr6.1kg.phase3.v5a.b37.bref3 \ map=plink.chr6.GRCh37.map \ out=immuno_chr6_imputed \ nthreads=16 \ ne=20000 \ impute=true \ seed=-99999
The data was passed down to me and i was told that the appropriate reference genome to use is the hg19 (GRCh37) build. When I run this script, i get the following error.
ERROR: Reference and target files have no markers in common in interval: 6:63979-21294564
Is there a way troubleshoot this? I queried my dataset based off position values and the interval 63979-21294564 is about 800 samples out of 8894.
Any help would be greatly appreciated!