Effect of --slam-seq 2 parameter in NextGenMap call?

[isaacvock]

Hello @t-neumann,

I recently noticed that in SLAMDUNK's call to NextGenMap, it by default includes the parameter setting --slam-seq 2. I was unable to find any information about this parameter on the NextGenMap wiki or parameter documentation printed when calling ngm with no other options or input. The (fantastic) SLAMDUNK documentation mentions something about an altered scoring function, which sounds really useful so I wanted to see if you knew any more details about what this parameter option does? I recognize that this question is probably more appropriate for the NextGenMap folks, and I posted a similar question on their Github, but their is a lot less recent activity there than here so I thought I'd try both.

Thank you, Isaac

[t-neumann]

Hi Isaac,

the --slam-seq 2 parameter introduces an adapted scoring matrix that does not penalize T>C mismatches as indicated in Table 1 of the Slamdunk paper. Hope that helps.

Tobi

[isaacvock]

Ah should've known to look there. Thank you very much!