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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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What is the default mindepth ? #120

Closed Hugsh closed 1 year ago

Hugsh commented 1 year ago

Hello,

Using the "artic minion" command, I'm wondering about if there is a default value for the minimum depth.

To be more precise, searching into the code I deduced that the choice for a nucleotide to be fixed to "N" in the final sequence is done at the depth mask level and thanks to the associated script "make_depth_mask.py". Then I found the "minDepth" parameter I suspect to be the little guy I was searching for.

We are actually analyzing ambiguous sequences and really need to go into detail. I don't know if I'm close to the answer or even missing an obviousness but choose to ask you.

Can you please tell me where to find this minimum depth info ?

Best regards

BioWilko commented 1 year ago

Hello the minimum depth default value is 20x as can be seen here: https://github.com/artic-network/fieldbioinformatics/blob/98241267d65eb76a98d11f3e41b6aeb71da68253/artic/make_depth_mask.py#L181

Hugsh commented 1 year ago

Dear @BioWilko,

Indeed, It's too bad I didn't zoom out the code.

Many thanks for your answer !

I have a practical example of a sequence which seems covered (according to the "coverage_mask.txt" file and the trimmed sorted bam visualization on IGV) on a range of positions but with "N" in the final consensus sequence.

Do you wish me to open a new issue for that or do you prefer to modify the present one ?

BioWilko commented 1 year ago

Can you check the failed variant VCF? If a variant fails filtering it is replaced by an N in the consensus. If that is the case it is the pipeline functioning as intended.

Hugsh commented 1 year ago

The linked variant is in the corresponding [id].fail.vcf as you suggested.

Thank you for the precision and your helpful support !

Have a great day.