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Welcome to the Wiki documentation of the SPACCa pipeline!

SPACCa is a Snakemake-base Pipeline for the Analyses of ChIP-seq data in Cancer samples. It allows the mapping of fastq files (both paired- and single-end) as well as other downstream analyses starting from the bam files (i.e., mapping filtering, sample correlation, peak calling). The latter, include data normalization, peak calling, GC-bias correction, Copy Number Variation (CNV) detection and signal correction and, identification of SNP/InDel at ChIP-seq peaks.

1. Introduction
2. Installation and dependencies
3. DNA mapping
4. Conversion of CRAM-to-BAM
5. Peak calling and normalization
6. GC bias correction
7. Copy Number Variation detection
8. SNP and InDel detection
9. Example for testing
10. Troubleshooting
11. Package info and releases
12. Citations

Fun fact: in italian slang when something "spacca" it means that it rocks.