I am running into an issue while doing Imputation with Beagle 5 and not sure what is causing the error. I have vcf files converted from PLINK by the following command
./plink --bfile qcd_in --chr 20 --recode vcf-iid --out qcd_chr20
This creates a VCF file
qcd_chr20.vcf which I am using as input in Beagle 5 for imputation.
The command I am running is as follows:
java -Xmx20g -jar beagle.28Jun21.220.jar gt=qcd_chr20.vcf ref=phase3.chr20.GRCh38.GT.crossmap.vcf.gz map=plink.chr20.GRCh38.map chrom=20 out=imputed_qcd_chr20
The error I get is the following:
java.lang.IllegalArgumentException: No VCF records found in the specified interval. Check chromosome identifier and interval: 20 at vcf.IntervalVcfIt.<init>(IntervalVcfIt.java:55) at main.Main.lambda$refSupplier$1(Main.java:292) at vcf.WindowIt$Reader.run(WindowIt.java:243) at java.lang.Thread.run(Thread.java:745)
The above is true for all the chromosomes. Can anybody help in resolving this issue? Am I missing something while recoding Plink files to VCF?