Missing MM and ML Tags in Output BAM File from Paraphase (3.2.1)

[shubhambinf1987]

Hello,

I am currently using Paraphase version 3.2.1 and have encountered an issue. The output BAM file does not retain the MM and ML tags present in the input BAM file. Is there a way to configure Paraphase to preserve all input tags while also adding the HP tags?

[xiao-chen-xc]

Hi @shubhambinf1987 Yes I will add the tags in the next release.

[xiao-chen-xc]

Hi @shubhambinf1987, Paraphase v3.3 is released. The Ml/Mm tags are now in the Paraphase output bam.

[shubhambinf1987]

Hi , I have 2 follow up questions

1. Is it okey to use paraphase on ONT adaptive sampling reads ( targeted ) and do I need license or official permission to do that ?
2. When applying to ONT Adaptive sampling, CN calls for SMN1/2 seems to underestimate at times ( specially for >2 copies ) , even when passed with --targeted parameter, is there a way to fix that ?