Implemented code for the reanalysis of somatic APP retrotransposition originally claimed by Lee at el (Nature, 2018). Modules for two different analyses--detection of intra-exonic junctions (IEJs) and estimation of APP gencDNA fraction--are provided. A detailed description of our analysis is available in our bioRxiv paper (https://bit.ly/35Kgfbu).

[ Basic usage ]
• Detection of IEJs connecting APP exons
java -jar somaticAPP.jar -D -b input.bam [optional_arguments]
* Input data: PRJNA577966
* The input bam should be mapped to APP751.fa (provided in the 'data' folder) and sorted by read name after mapping

• Estimation of gencDNA fraction
java -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.

Try -h or -? options to get detailed descriptions for optional input parameters

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2019-10-17
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