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Filter Error: Bad input: We encountered a non-standard non-IUPAC base in the provided:"10"
I'm using GATK to call SNPs for a F2 mapping population design using GBS. So, my reference is derived from all my GBS lines. Running the GATK using UnifiedGenotyper worked great, generating perfectly valid output and a viewable vcf (in excel and IGV). However, I'm now trying to filter for just biallelic SNPs using SelectVariants, and I keep getting this error:
ERROR MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'
I'm using the same reference files (.fa, .fai, .dict, etc) as for the GATK, and haven't modified them in anyway. They've never been processed by Windows software, and I can't seem to find any non-standard formatting or data (at least in a cursory look). Any thoughts?