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Patchwork specifications


Unique identifier OMICS_02118
Name Patchwork
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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Publications for Patchwork

Patchwork citations


The macro evolutionary events in esophageal squamous cell carcinoma

PMCID: 5762549
PMID: 29348864
DOI: 10.18632/oncotarget.22625

[…] (nmf) and model selection approach to extract mutational signatures from the wgs data of 17 escc tumors with gd []. the somatic cnvs of sample pairs were identified by algorithm based on patchwork []. segmentation results were then used for the subsequent analysis. gistic algorithm was used to infer recurrently high amplified genomic regions. absolute copy number was estimated […]


The genomic dynamics during progression of lung adenocarcinomas

J Hum Genet
PMCID: 5537414
PMID: 28381877
DOI: 10.1038/jhg.2017.40

[…] based on homology and sequencing features. after filtering out germline events and other artifacts, we got the final somatic structural variants and further generated fusion genes., we used patchwork to identify copy number alterations from nine primary and metastatic tumors. segmentation results were then used for the subsequent analysis., we inferred bfb events from the meerkat […]


Identification of Medium Sized Copy Number Alterations in Whole Genome Sequencing

Cancer Inform
PMCID: 4356486
PMID: 25788829
DOI: 10.4137/CIN.S14023

[…] counts are calculated and compared to a selected reference value, which typically is a matched control. tools such as segseq, readdepth, hmmcopy, bayesian information criterion sequencing (bic-seq), patchwork, varscan2, control-freec use this approach. some of the algorithms also include steps to handle systematic biases such as genomic mappability (control-freec, readdepth, and hmmcopy) […]


The Mutational Landscape in Pediatric Acute Lymphoblastic Leukemia Deciphered by Whole Genome Sequencing

Hum Mutat
PMCID: 4309499
PMID: 25355294
DOI: 10.1002/humu.22719

[…] experiment ids are listed in supp. . somatic copy number alterations (cnas) were called using bic-seq [xi et al., ], controlfreec [boeva et al., ], dwac-seq (, and patchwork [mayrhofer et al., ]. cnas detected by at least two programs were retained. all variants were annotated against the ensembl database., strand-specific libraries for rna-sequencing (rna-seq) […]

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