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Old 07-26-2020, 11:10 PM   #1
dnya
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Location: Europe

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Default calling SNVs in shallow WGS data from liquid biopsy

Hi All,

could there be any reasonably reliable SNV calling approach in the following scenario: I have shallow (1-3x) WGS sequencing data from liquid biopsy samples from cancer patients, where the ctDNA fraction is very low (1% AF) and that contains the SNVs that I would be interested in. I don't have the white blood cell (aka normal sample) data for the patients, just the pure, sequenced blood plasma (mix of cfDNA + ctDNA).

I know, it's not a great setup, but this is what I've got to work with for a project.

Any suggestion (even if it's just talking me out of doing something crazy like this) is appreciated!
Thanks!
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liquid biopsy, shallow coverage, snv, variant calling, wgs

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