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?
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?