GATK Somatic CNV Tumor only calling
Dear GATK team.
I am trying to perform somatic CNV calling on a custom panel of approximately 1,200 genes in tumor-only mode.
I found the following workflows for somatic CNV calling (recently updated), but they seem to work only for tumor samples with matched normal cases.
https://gatk.broadinstitute.org/hc/en-us/articles/360035531092--How-to-part-I-Sensitively-detect-copy-ratio-alterations-and-allelic-segmentshttps://gatk.broadinstitute.org/hc/en-us/articles/360035890011--How-to-part-II-Sensitively-detect-copy-ratio-alterations-and-allelic-segments
Could you please let me know if there are any options for tumor-only samples in this workflow, or should I use a different workflow?
Thanks In Advance
Fazulur Rehaman
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Somatic CNV workflow requires a Panel of Normals to compare for copy number aberrations therefore you cannot perform a tumor only (cohort) calling using this method.
I hope this helps.
Regards.
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Dear GATK team,
Thank you so much for your quick response.I have data for 15 healthy control samples from which i can create panel of normals. However these healthy controls are not from same tissue. Could you please let me know whether I can compare cnv abbreviations in tumor-only with 15
healthy panel of normals?
Thanks In Advance
Fazulur Rehaman -
Hi again.
The more samples added to the control the better but if you only have 15 samples you can definitely give it a go. You might need to setup a higher/lower fold change threshold for certain events due to low number of normals provided.
I hope this helps.
Regards.
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Dear Gokalp Celik,
Thank you so much for confirming.
Thanks & Regards
Fazulur Rehaman
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