WES NGS Quality Control

Question

[SurdanBurasi]

I'm on a bioinformatics team. my team is doing bioinformatics on next generation sequencing. Our work was adapted to the GATK best practice, but we could not figure out how to check the quality and accuracy of the data. what should we do for quality control?

[ATpoint]

Which data? Exome-seq, RNA-seq, ChIP-seq, scRNA-seq? Some details would be good.

[SurdanBurasi]

whole exome sequence

Answer 1

[igor]

There is a previous discussion with good suggestions: QC for Whole Exome Sequence Data

Also, this page lists many relevant metrics: https://genestack-user-tutorials.readthedocs.io/tutorials/WES_data_analysis/