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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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To call variants from multiple amplicons in a sample #697

Closed ckhithesh closed 4 years ago

ckhithesh commented 4 years ago

Hi team, I'm looking to call the variants from multiple amplicons in single sample. Clearly a sample contains 10genes to call variants using nanopolish variants. And I don't want to mention the regions (-w).

Thanks in advance Regards Hithesh

jts commented 4 years ago

Unfortunately you will have to specify the regions with -w.

ckhithesh commented 4 years ago

Dear Team, Any suggestion on parameters for SNP calling (multiple contigs). Regards Hithesh

jts commented 4 years ago

It is hard to help without information about your sample and sequencing data so I suggest using the defaults.

ckhithesh commented 4 years ago

Dear Simpson, My sample details are 6 samples. where a sample consists of 5 amplicons and I have to call variants of all 5 amplicon in a sample. As if I used -w it will work for specific region. How to retrieve variants for 5amplicons from a sample. Regards Hithesh

jts commented 4 years ago

Hi,

You will have to run nanopolish 5 times, once for each region.

Jared

ckhithesh commented 4 years ago

Dear Jared, Thank you for the reply! I have one more question regarding the variant call for the complete genome. I have a genome of around 500 scaffolds. So, please let me know how to do for this?

Regards Hithesh

jts commented 4 years ago

Hi @ckhithesh,

We provide an example of running over many windows of a genome here:

https://github.com/jts/nanopolish#computing-a-new-consensus-sequence-for-a-draft-assembly

This is for consensus calling but you should be able to adapt it to call variants instead (remove the --consensus flag, add any other options you need).

Jared