The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
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.