- Graphical assessment of structrial variants using 10x genomics data
- Han Fang (email@example.com)
- Srividya Ramakrishnan (firstname.lastname@example.org)
- Fritz Sedlazeck (email@example.com)
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
python topsorter.py $vcf
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>