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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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MLST for diploid microbes #106

Closed labrat9 closed 6 years ago

labrat9 commented 6 years ago

Dear authors,

I am testing srst2 for MLST of Candida albicans. I got the ST types but realised that for each gene, the heterozygous nucleotides have been omitted from downstream analysis. Due to this omission, the coverage for that particular site, where heterozygosity exists, drops by half.

Is there an option (a way) for consensus allele to include non-AGTC nucleotide to indicate heterozygosity?

Thanks.

katholt commented 6 years ago

The scoring algorithm is specifically designed for haploid allele typing, I would not recommend using it for MLST of diploid organisms.

If you just want to extract consensus sequences for your MLST loci, you can do this by feeding bam alignments to programs designed to do that (e.g. samtools)