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parklab / NGSCheckMate

Software program for checking sample matching for NGS data
MIT License
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function to start with already generated .ncm files? #36

Open imcoleman opened 3 years ago

imcoleman commented 3 years ago

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 commented 3 years ago

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 -O <-N PREFIX>

Best regards, Sejoon Lee

imcoleman commented 3 years ago

Thanks @sejooning!

imcoleman commented 3 years ago

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.