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
[email protected]
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