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vahidAK / NanoMethPhase

Methylation Phasing for Nanopore Sequencing
GNU General Public License v3.0
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Reproduce Fig.4 a-b and Additional file 4. #11

Closed liuyang2006 closed 2 years ago

liuyang2006 commented 2 years ago

Dear author,

Thank you for providing codes of your paper.

I have a small issue to reproduce Fig. 4a-b, and additional file 4. My phased results for two haplotypes are slightly bad than your paper's results.

Here, I only use Nanopolish+Clair + WhatsHap, I haven't use SNVoter. I am not sure if this is the reason. I have no idea of how to apply SNVoter (after Clair, and before WhatsHap) here. If you can provide me some sample script for how to use SNVoter to improve the results, that would be a great help! Thank you!

Best, Yang

vahidAK commented 2 years ago

Hi Yang,

We have provided instructions for SNVoter in its repo (We used this on Clair, not the new development of it Clair3. Moreover, SNVoter works on low coverage data and older versions of the guppy (<4.3) and we have not tested it on newer versions):

https://github.com/vahidAK/SNVoter What dataset/sample are you using?

BTW, if you use new guppy and Clair3, SNVoter is not required. For WhatsHap, I also recommend using only high-quality SNVs for phasing.

Best, Vahid

liuyang2006 commented 2 years ago

Thank you very much for your reply, @vahidAK!

I am using same NA19240 run1 dataset, processed by Clair3+WhatsHap. But I use all SNVs instead of high-quality score. Just as you mentioned, this maybe the reason.