MMR for variant calling ?

Question

[thomasbersez]

Hi,

Does anyone ever used MMR or others ambiguous reads resolution tools on bam files before to do variant calling? Does it improvement results accuracy?

Thanks for help !

[colindaven]

I tried AlignerBoost once https://github.com/Grice-Lab/AlignerBoost but never really got it established or saw major advantages. However, I do see opportunities for improving short read mapping quality estimates, since incorrect alignments cause many problems in my work.