AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
1.3.r8 adds breakpoint microhomology detection from alignments marked as supplementary (not just secondary). Also tweaks sashimi plot visualization of CN.
1.3.r7 refines the CN segmentation shown in the visualizations to prevent mismatches between displayed CN and coverage. Also allows SV VCF to use "." in the FILTER field instead of only "PASS". MOSEK convergence criteria relaxed slightly to prevent rare termination issues.
jluebeck
commented
3 months ago
1.3.r8adds breakpoint microhomology detection from alignments marked as supplementary (not just secondary). Also tweaks sashimi plot visualization of CN.1.3.r7refines the CN segmentation shown in the visualizations to prevent mismatches between displayed CN and coverage. Also allows SV VCF to use "." in the FILTER field instead of only "PASS". MOSEK convergence criteria relaxed slightly to prevent rare termination issues.