Hello,
I'm doing DNA targeted resequencing. The target were enrichted by hybridization capture. In my bioinformatics pipeline I collect quality metrics wit CollectHsMetrics from picard tools.
From time to time there are some samples that have very different values for the GC_DROPOUT and AT_DROPOUT metrics compared to the other sample within the run. These samples made some problems in CNV analysis.
Is there a way to correct the coverage values for my target regions, taking the GC/AT-Bias into account?
fin swimmer
There is an implementation of the Benjamini & Speed method in deeptools, named computeGCBias, and a downstream tool, correctGCBias, that you might want to check out. Unfortunately I cannot tell you if this correction is necessary or beneficial on your dataset.
Thank you for your answer ATpoint.
I will have a look at this in the next few days. But it looks promising.
fin swimmer
Hello ATpoint,
a played a bit around with computeBias and it seems to make exactly what I need. If you move your comment to an answer I could mark it as accepted.
Thanks again.
fin swimmer
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