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Hey guys,
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 seems that there is an 'M' in the bam file due to the existence of degenerate bases. By the way, I used Novoalign to do the alignment. However, I did not meet the same problem when I used the same bam file and samtools to call variants.
I have reported this problem to GATK, and followed the instructions. Unfortunately, I still have not solved my problem yet. Here is the link with GATK forum:https://gatk.broadinstitute.org/hc/e...t_360012136691
I would be happy if anyone can help and discuss with me.
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 seems that there is an 'M' in the bam file due to the existence of degenerate bases. By the way, I used Novoalign to do the alignment. However, I did not meet the same problem when I used the same bam file and samtools to call variants.
I have reported this problem to GATK, and followed the instructions. Unfortunately, I still have not solved my problem yet. Here is the link with GATK forum:https://gatk.broadinstitute.org/hc/e...t_360012136691
I would be happy if anyone can help and discuss with me.