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
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.
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
Distributed under the MIT License.