post-processing step

[CocoMlle]

Hello,

Thanks for your amazing job this is really helpfull ! I have one question about post-processing steps. I didn't find more informations about it in your paper, then what is the impact on the results if we use data with recalibration and so on?

Thanks for your answer !
Best regards,
Marine

[egor-dolzhenko]

Hi Marine,

Thank you for using EHdn! We tested the program without applying any post-processing steps to the input BAM files. However, as long as the post-processing steps do no change alignment positions or mapping qualities of the reads, EHdn should still work fine.

A good (but time consuming) way to test that your pipeline produces BAM files compatible with EHdn, is to obtain some samples with known repeat expansions (for example these data from this paper), reprocess them with your pipeline, and then confirm that EHdn can still detect the expansions.

Did I answer your question?

Best wishes,
Egor

[CocoMlle]

Hi Egor,

Yes thanks for your answer i was just afraid maybe it could change the outcome.

Best wishes,
Marine