Increase min depth of coverage for Flu assembly using IRMA

[molly-hetheringtonrauth]

🆒

📌 Explain the Request

Regarding the flu module of the wf_theicov_illumina_pe.wdl:
Based on the task_irma.wdl you are pulling the consensus fasta files from the main sample directory output from IRMA. These fasta files use a min depth of coverage of 1x for base calling. Based on my conversations with CDC, you want to set the MIN_CONS_SUPPORT="50" in the irma config file which will use a min depth of coverage of 50x for base calling. And here's the tricky part once you have set the config file- the consensus fasta files in the main sample directory output from IRMA still will only reflect base calling using a min depth of coverage of 1x. The consensus fasta files in the amended_consensus directory will have the consensus fasta files that reflect base calling using a min depth of 50x. Additionally the consensus fasta files in the amended_consensus directory will also use IUPAC nucleotides for mixed base calls (I'm not sure what the minor allele frequency has to be in order for it to be considered a mixed base call). And finally the conesnsus fasta files in the amended_consensus directory will be named according to their genbank segment number (note the difference in segment number for PB1 and PB2 for Flu A and Flu B):

FluA=["PB2"]="1" ["PB1"]="2" ["PA"]="3" ["HA"]="4" ["NP"]="5" ["NA"]="6" ["MP"]="7" ["NS"]="8" 
FluB=["PB1"]="1" ["PB2"]="2" ["PA"]="3" ["HA"]="4" ["NP"]="5" ["NA"]="6" ["MP"]="7" ["NS"]="8" 

You can see how I handled using the conensus fasta files in the amended_consensus directory at our CDPHE-bioinformatics/CDPHE-influenza/ github repo,.

[kevinlibuit]

Thank you for pointing this out, @molly-hetheringtonrauth. Definitely a lot of non-intuitive action happening under the hood here.

We appreciate the insight and are taking a closer look at things now!