Can you please provide
a) GATK version used :126.96.36.199
b) Exact GATK commands used : HaplotypeCaller
c) The entire error log if applicable. : java.lang.IllegalArgumentException: Unexpected base in allele bases 'ATTTTTCTGAATCCCTTTCAAATCAGGACAAGAACTAGAAATGTCTATACAGGTTTAATATGAAGTAAAGAAAATGTTTTTCATTTTCTTGATTTATTTCTGAATTCAGCTTGCTCTTCATTAGCGCTACATAGCTGMCTTATTATTCGTGGTCCCCTATGACCCCCTGATCATTTTCCCTGAGGGTGCATATTTATTCACTAACTATGTTACAATCATGTGATCTGCTGGATTTTTTCTGATAGTCTACTCTAGATTTGTTCTAAATTAATAAA'
I apologize for the possibly stupid question I will ask. The problem is that I met the error "java.lang.IllegalArgumentException: Unexpected base in allele bases '...TGMCT...'" when I was using HaplotypeCaller to identity the SNPs and InDels. It is apparent that there is an 'M' in the bam file due to the existence of degenerate bases. I wonder how can I deal with or skip this region to continue calling process.
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