Dear Samtools developers,

I recently noticed that in source code of bam2bcf_indel.c, genotyping different indel alleles are based on their insertion/deletion length. However, if there are two non-reference alleles with the same insertion/deletion length, such as ref:G, non-ref1:GAC and non-ref2:GGT, when using bcftools view -A to release all variant alleles, only one of them with max read count will be displayed in the results. If I am right, I think the indel genotyping should involve the sequence (AC/GT) into consideration.

Best,

Xiaobin