hanfang / Topsorter

Graphical assessment of structrial variants using 10x genomics data

Topsorter

- Graphical assessment of structrial variants using 10x genomics data

Contact

• Han Fang ([e-mail])
• Srividya Ramakrishnan ([e-mail])
• Fritz Sedlazeck ([e-mail])

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Topsorter

Traversing & finding the longest path (most confident haplotype) in a weighted directed acyclic graph (DAG).

• At the initial construction step, it splits regions of a chromosome by structural variants and creates a weighted DAG.
• Then it updates the weights of the edges according to barcodes information (and/or other quality metrics) from the script barcode_profiles.py.
• Finally Topsorter performs topological sorting of the graph and finds the longest path (the most confident haplotype).
• Input: vcf file
• Output: PDF files of graphs for each chromosme, longest paths
• Command: python topsorter.py $vcf

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BarcodeProfiler

Building barcode profile for the alignments and count the overlapping barcodes for every split region of a chromosome

• Extract alignments from every split region in to a bam file and index them

• Identify the barcodes in each of these split regions and count number of reads per barcode

• Count the barcode overlaps between the split regions of interest

• Input: Phased bam file from 10x data, Constructed split regions in bed format using Topsorter class (func exportVCFBed )

• Output: directory containing files overlapping_reads.bam overlapping_reads.bam.bai reads_barcode_profile.txt barcode_overlaps_between_regions.txt

• Command: ./barcode_profiles.py -bam <input phased bam> -bed <input constructed bed file> -o <output dir name>