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ShixiangWang / gcap

GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data and absolute copy number profiles. https://shixiangwang.r-universe.dev/gcap
https://shixiangwang.github.io/gcap/
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support mouse data #31

Closed ShixiangWang closed 1 year ago

ShixiangWang commented 1 year ago

NOTE: ASCAT does not support mouse genome, I need further check and generate a new solution for (allele-specific) copy number calling in mouse genomes.

ShixiangWang commented 1 year ago

This feature is designed for ecDNA PDX project, and considered as an independent pipeline for journal F1000 or preprint services.

ShixiangWang commented 1 year ago

Calling tools:

Reference: https://xsliulab.github.io/PC_CNA_signature/#copy-number-calling

Input data: bam

All other downstream steps should be automatically processed.

ShixiangWang commented 1 year ago

The issue is closing due to https://github.com/ShixiangWang/gcap/pull/32