Can Manta be used for haploid genome?

Illumina / manta

Structural variant and indel caller for mapped sequencing data

GNU General Public License v3.0

404 stars 154 forks source link

Can Manta be used for haploid genome? #194

Closed souravnayak closed 5 years ago

souravnayak commented 5 years ago

I am working with haploid microbial genome. I have a set of genome sequenced. I want to look for structural variations within the population. Can I use MANTA for calling the SVs?

ctsa commented 5 years ago

It should work reasonably well in practice. Compared to a true haploid model, the diploid scoring model genotype confidence for a variant will grow more slowly as a function of depth, but that should only matter for low-depth sequencing. If you're actually evaluating a pooled sample then you might consider the tumor-only calling mode instead.