rmcolq
0 depth reported across many genes in the pandora consensus
Putting this here as a reminder until I am able to get a minimal example showing this. It seems that the quality string in the pandora consensus file says that all bases are 0 depth for many genes. I do not think it is a major issue because most people will not be using Pandora at the same level as me but it is something to be aware of. My work around is remapping all of my reads to the pandora consensus using minimap2 and estimating the coverage of each base from that.
Apologies I realise I never actually collected an example of this happening. From my recollection it happens pretty frequently though, like multiple times per sample.
On 8 Sep 2025, at 23:09, Zamin Iqbal @.***> wrote:
[https://avatars.githubusercontent.com/u/6476513?s=20&v=4]iqbal-lab left a comment (iqbal-lab-org/pandora#357)https://github.com/iqbal-lab-org/pandora/issues/357#issuecomment-3268185631
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