When running Genotypeharmonizer, I come across an odd error:
GenotypeHarmonizer.sh --input file --o file2 -r reference.file -R VCF
Input data loaded
Reference data loaded
Beginning alignment
Iteration 1 - 10,000 variants processed
Iteration 1 - Completed, non A/T and non G/C SNPs are aligned 8,723 found and 4,372 swapped
Iteration 2 - Skipped, non A/T and non G/C SNPs are not LD checked
Iteration 3 - Completed, non A/T and non G/C SNPs are aligned. Extra LD check skipped
Swapped 0 A/T or G/C variants based on LD patterns
Alignment complete
Excluded in total 3,723 variants during alignment phase
Writing results
Error writing output data: Trying to write alleles [G] for G\A SNP
I've looked online, but the documentation especially for this type of error seems to be sparse. Any suggestions on how to correct or learn more about the issue? I added in the "--debug" variable too, but there wasn't a difference in output.
