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Clinical-Genomics-Lund / nextflow_tumwgs

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ID_SNPs based sample identification #19

Open sailepradh opened 9 months ago

sailepradh commented 9 months ago

There are cases in the lab where the samples are mixed up, which causes further issues in the pipeline and analysis. We want our workflow to catch this mix-up earlier in the pipelines. To this end, lab have implemented rsID based fingerprinting of the samples. @A97paupic have developed software packages that can take the bam files to provide sample percent identity that could be used to access the sample identity.

So here are the task list that needed to be integrated in the current tumor-normal somatic WGS analysis.

A97paupic commented 9 months ago

The software is being validated by Magdalena B Holgersson on paired samples just to find a trade off threshold as there are different types of challenges dealing with bad samples. As soon as she has arrived at a good estimate we can integrate it into the somatic WGS pipeline as well as the other ones that could benefit from such comparison.