Processing VCF file Framework of Structural Variant (SV)

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This tool set provides below function to display, compare,merge, filter the vcf files of structural variants(SVs) or SNPs

【SV_stat_vcf.py】Display Statistical genotypes information and Length distribution of structural variants.
【2】Merge SVs into VCF file of One Sample.

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【1】 SVs' genotypes statistics
Two main steps:
Display Statistical genotypes information and Length distribution of structural variants.
(1)Statistical genotypes information fo structural variants from VCF file
Display SV statistical result in Terminal
(2)Generate (phased_SV_length_destribution) in CSV
【2】Merge VCF (these vcf-files represent one sample).

Usage

Run the script like:

$ python3 SV_stat_vcf.py -v MY_SV.vcf 

Option : Use My_len_destribution.csv

You can display Density Plot by R :

path = "My_len_destribution.csv"
vcf_density = read.csv(path, header=T, sep = '\t',encoding = 'UTF-8')

ggplot(vcf_density, aes(x=SVLEN,group=CHR, fill=label))+
  geom_density(color="darkblue", fill="lightblue")

Note

This tool adapts to duel with SV vcf-file generated by structural variants (SVs) software cuteSV,etc..