Is your feature request related to a problem? Please describe
Allowing for different trimming based on library strandedness.
pileupCaller allows us to use untrimmed data for ssDNA libraries without damage affecting the genotypes. That means that ssDNA non-UDG libraries do not need trimming, and can be run with --bamutils_clip_none_udg_{left,right}=0. However, that becomes a problem when ssDNA and dsDNA non-UDG libraries are combined in a single run, since when genotyping from untrimmed data for the latter damage will heavily affect the genotypes.
Describe the solution you'd like
Add library construction specific trimming options, e.g. bamutils_clip_{single,double}_{none,half}_udg_{left,right}. This would allow trimming flexibility and let users utilise a single set of parameters across different types of data.
Describe alternatives you've considered
It is possible to create separate runs for dsDNA and ssDNA libraries, but that sounds less elegant a solution, especially for applications that are potentially (semi-)automated.
Is your feature request related to a problem? Please describe
Allowing for different trimming based on library strandedness.
pileupCallerallows us to use untrimmed data for ssDNA libraries without damage affecting the genotypes. That means that ssDNA non-UDG libraries do not need trimming, and can be run with--bamutils_clip_none_udg_{left,right}=0. However, that becomes a problem when ssDNA and dsDNA non-UDG libraries are combined in a single run, since when genotyping from untrimmed data for the latter damage will heavily affect the genotypes.Describe the solution you'd like
Add library construction specific trimming options, e.g.
bamutils_clip_{single,double}_{none,half}_udg_{left,right}. This would allow trimming flexibility and let users utilise a single set of parameters across different types of data.Describe alternatives you've considered
It is possible to create separate runs for dsDNA and ssDNA libraries, but that sounds less elegant a solution, especially for applications that are potentially (semi-)automated.