Working With VCFs

The VCF Class

panVCF.VCF(file)
parameters:
file - The VCF file which you want to load into panVCF

Data

VCF.vcf
Pandas dataframe of vcf data, excluding headers
VCF.geno
Pandas dataframe of genotype data
VCF.head()
Returns the headers for the vcf

Changing Reference Genome

VCF.change_base(old_reference_file, new_reference_file, chrom)

Used when the reference genome of a vcf file must be changed. Must be done one chromosome at a time (vcf can have more than one, but the fasta files can only have one).

parameters:

old_reference_file - The fasta file that contains the data for the chromosome of interest that serves as the reference for the current vcf

new_reference_file - The fasta file that contains the data for the chromosome of interest that is the desired reference for the vcf

chrom - The chromosome of interest. For example ‘22’ or ‘Y’

output:
VCF - a new vcf object with a new VCF.vcf and VCF.geno

Indels

isindel(line)
parameters:
line - the line of data to analyze
output:
Boolean - True if line is an indel, if not, False