Can ichorCNA be used for analyzing 150 bp paired-end reads?

broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

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Closed ciciyun closed 5 years ago

gavinha commented 5 years ago

Hi @ciciyun

Yes, ichorCNA can be used to analyze 150bp paired-end reads. The readCounter step treats the mate reads independently.

Best, Gavin