Haplotyper creating vcf files but stopping before reading SNPs
Please forgive me if this is a naive question because I am new to gatk.
I am using HapltoypeCaller to call SNPs using a pseudo reference I have created from my sequence data (no reference available and the data is bait capture not whole genome). When I invoke HaplotypeCaller I get the following error after what appears to be normal work:
Exception in thread "main" java.lang.IncompatibleClassChangeError: Inconsistent constant pool data in classfile for class org/broadinstitute/hellbender/transformers/ReadTransformer. Method lambda$identity$d67512bf$1(Lorg/broadinstitute/hellbender/utils/read/GATKRead;)Lorg/broadinstitute/hellbender/utils/read/GATKRead; at index 65 is CONSTANT_MethodRef and should be CONSTANT_InterfaceMethodRef
The vcf files I am asking to be made are in fact made but they are devoid of SNP data.
Thanks for the help and advice.