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Can I get compy number between white blood cell bam and adjacent normal tissue bam

Open shenhaizhongdechanrao opened this issue 1 year ago • 1 comments

hi, Can I get compy number between white blood cell bam and adjacent normal tissue bam. Is it suitable for samples between non-tumors?

shenhaizhongdechanrao avatar Oct 03 '24 09:10 shenhaizhongdechanrao

Could work, depending on the cancer. Is this leukemia/lymphoma?

If you're not sure about your "normal" samples, you could try running CNVkit with a "flat" reference on those samples to see if they have any recurrent, large-scale copy number alterations. If they do, you can omit those samples or overwrite the altered regions with a log2 value of 0.0.

etal avatar Nov 13 '24 06:11 etal