Hi everyone,

I am trying to run the Beagle 5.4 software where it needs to read a VCF file. The error message I have is:

Exception in thread "main" java.lang.IllegalArgumentException: VCF record format error: 1       131079320     BHD0100437271      G       A       .       PASS    .       GT
    at vcf.VcfRecGTParser.ninthTabPos(VcfRecGTParser.java:87)
    at vcf.VcfHeader.isDiploid(VcfHeader.java:73)
    at vcf.RefIt.<init>(RefIt.java:130)
    at vcf.RefIt.create(RefIt.java:97)
    at vcf.RefTargSlidingWindow.refIt(RefTargSlidingWindow.java:122)
    at vcf.RefTargSlidingWindow.<init>(RefTargSlidingWindow.java:81)
    at vcf.RefTargSlidingWindow.instance(RefTargSlidingWindow.java:70)
    at main.Main.slidingWindow(Main.java:129)
    at main.Main.main(Main.java:107)

What I get from the message is that the VCF record format in the 9th column (FORMAT) is not what the software expects. The Beagle software manual addresses:

gt=[file] specifies a VCF file containing genotypes for the study samples. Each VCF record must contain a GT (genotype) format field.

Therefore I supposed that I prepared the data correctly, you see the the first two rows of the VCF file:

##fileformat=VCFv4.1
##filedate=20180306
##source="beagle.22Jul22.46e.jar
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="estimated ALT dose [P(RA) + P(AA)]">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype Probability">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  DE007990097800  DE007990143236  DE007000630845   DE007000630848 DE007990011508  
1   131079320   BHD0100437271   G   A   .   PASS    .   GT  1|1 1|1 1|1 1|1 1|1 
1   131206718   BHD01000300 G   A   .   PASS    .   GT  1|1 0|1 1|1 1|0 0|1 

I would appreciate if you share with me any idea and guidance on the issue.

UPDATE: Actually I realized a problem in which the FORMAT column is GT so it expects genotype data while the provided information is Dosagae (DS) type. I'd appreciate if you confirm if technically I can modify the FORMAT column manually or not?