STAR overwrite hard coded aligner options in case of bamRemoveDuplicatesType UniqueIdentical is not possible

[NderBinf]

I ran into a problem when I used the alignerOptions for STAR

If I need to run twopassMode with: bamRemoveDuplicatesType UniqueIdentical this will according to the manual only work with outSAMtypy BAM SortedByCoordinate. STAR MANUAL

If I supply:
alignerOptions "--twopassMode --sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --bamRemoveDuplicatesType UniqueIdentical"

I will run into two problems:

1. hardcoded alignerOptions in your code:
   --sjdbOverhang 100
   --outSAMunmapped Within
   --outSAMtype BAM Unsorted
   --outStd BAM_Unsorted \

2. your approach to use samtools for sorting

My aligner options contradict your hard coded outSAMtype BAM Unsorted.

Furhtermore: the code does not check for duplicate aligner Options (STAR however does so and fails) and unifies them. You could supply the hardcoded values in the manual, so that people know.

Thanks for the great tool.

Kind Regards
Nicholas

[katsikora]

Dear Nicholas,

thanks for sharing your issue. Do I understand correctly that it would be sufficient to make outSAMtype flag user-defined instead of hard-coded? If so, I can adjust the code.

Best wishes,

Katarzyna