function to start with already generated .ncm files?

[imcoleman]

Hello,
I have an application to run ngscheckmate iteratively on the same dataset when new data is added. It is easiest for me to use the fastq file workflow but it takes a considerable amount of time as the amount of data increases. Is there a way to run the program using existing .ncm files previously generated?
Thanks!

[sejooning]

Hello,
Thank you for using the NGSCheckmate.
We use "vaf_ncm.py" script to run NGSCheckMate based on "*.ncm" files .
Usage: python vaf_ncm.py -f -I <INPUT_DIR> -O <OUTPUT_DIR > <-N PREFIX>

Best regards,
Sejoon Lee

[imcoleman]

Thanks @sejooning!

[imcoleman]

Hi @sejooning,
I tried using "vaf_ncm.py" on previously generated ".ncm" files, and it ran without any error messages. However, some of the samples which had high correlations when run using the "ncm_fastq.py" now had zero correlation. These samples should be highly correlated, so I wondered if something is going wrong with the "vaf_ncm.py" correlation output. It also did not generate the "output_matched.txt" file.
Thanks for any advice you can provide.