Graphical assessment of structrial variants using 10x genomics data
Python
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Topsorter

- Graphical assessment of structrial variants using 10x genomics data

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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

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>