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Implemented framework with regard to the reanalysis in the case of somatic APP retrotransposition in the opening phase avowed by Lee at el (Nature, 2018). Modules for two different analyses--detection of intra-exonic junctions (IEJs) and estimation associated with APP gencDNA fraction--are provided. A detailed description of our analysis is available in this bioRxiv paper (https://bit.ly/35Kgfbu). [ Basic usage ]• Observation of IEJs bridging APP exonsjava -jar somaticAPP.jar -D -b input.bam [optional_arguments]* Input reports: PRJNA577966* The input bam should be mapped in order to APP751.fa (provided in the 'data' folder) and sorted by read name after mapping • Interpretation of gencDNA fractionjava -jar somaticAPP.jar -F -b input.bam -a BWA_PATH -s SAMTOOLS_PATH [optional_arguments]* Input data: PRJNA493258* The input bam should be a human-genome-mapped (hg38), coordinate-sorted, and duplicate-marked file. Reach -h or -? options to get detailed descriptions for non-compulsory input parameters

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