Beagle 5 error: No VCF records found in the specified interval

Question

[aritra90]

Hi,

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?

[WouterDeCoster]

It seems there is a space missing in qcd_in--chr.

[aritra90]

Thanks, that was a typo. I fixed it.

Answer 1

[aritra90]

Found the solution for anyone interested. The issue was in the reference file Chromosome IDs being "chr20" instead of "20" (as in the target file) -- hence the mismatch. Do --output-chr chrM in PLINK 1.9 VCF recode to avoid this error in BEAGLE.