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A method for visualizing VCF data on a circos plot (data is generated in a format easy to use with the Circos software)

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VCFStatistics

A method for visualizing VCF data on a circos plot (data is generated in a format easy to use with the Circos software)

Table of Contents
  1. Requirements
  2. Usage
  3. License

Requirements

These scripts have been tested with Python 2.7 and 3 and should work with either. These scripts requires a VCF file (with a depth field for certain metrics). The VCF file can be compressed with gzip or bgzip.

Usage

Find metrics for each individual in each window

  python VCF.stats.windowBased.v1.0.py -vcf file.vcf -win 10000 -depth 3 > statsfile.out

  To see the usage and get further information: python VCF.stats.windowBased.v1.0.py -h

Summarize data for groups and possibly output in a format that can be used with Circos software to visualize.

  python PartitionData.LsalSpecific.py -file statsfile.out -ind ind1,ind3 -avg no -out depth -win 10000 -chr no > output.txt

  To see the usage and get further information: python PartitionData.LsalSpecific.py -h

Optionally, identify regions that differ by missing genotypes between different groups (used for a specific project)

  python SexSpecific.LsalSpecific.py -file statsfile.out -ind1 ind1,ind3 -ind2 ind2,ind4 -win 10000 -fold 2
  
  To see the usage and get further information: python SexSpecific.LsalSpecific.py -h

License

Distributed under the MIT License.

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A method for visualizing VCF data on a circos plot (data is generated in a format easy to use with the Circos software)

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