vcf2pandas 0.1.0

Package to convert a vcf into a pandas dataframe.

vcf2pandas

vcf2pandas is a python package to convert vcf files to pandas dataframes.

Install

pip install vcf2pandas

Dependencies

• pandas (2.1.0)
• pysam (0.21.0)

Usage

Selecting all columns

from vcf2pandas import vcf2pandas
import pandas

df_all = vcf2pandas("path_to_vcf.vcf")

Selecting custom custom columns and samples

info_fields = ["info_field_1", "info_field_2"]
sample_list = ["sample_name_1", "sample_name_2"]
format_fields = ["format_name_1", "format_name_2"]

df_selected = vcf2pandas(
    "path_to_vcf.vcf",
    info_fields=info_fields,
    sample_list=sample_list,
    format_fields=format_fields,
)

Custom column ordering

vcf2pandas can select custom/specific:

• INFO fields
• samples
• FORMAT fields

And order the selected columns based on the input list.

E.g. The following list:

info_fields = ["DP", "MQM", "QA"]

Gets the columns (in that order)

INFO:DP    INFO:MQM    INFO:QA

Note that this only applies for INFO and FORMAT columns. That is, the samples will be ordered based on the VCF and not the input list.

Output

INFO and FORMAT headings

INFO:INFO_FIELD                     e.g. INFO:DP
FORMAT:SAMPLE_NAME:FORMAT_FIELD     e.g. FORMAT:HG002:GT

INFO fields not present for some variants

When certain INFO fields are not present for certain variants, vcf2pandas inserts a . instead in that cell. E.g. for vcf3_all.txt you can see INFO:GENE column has . for the first 7 variants.

Examples

Example vcf and output files (dataframes as a .txt file) are available in examples/

Example Usage

df1 = vcf2pandas("examples/vcf1.vcf")
df2 = vcf2pandas("examples/vcf2.vcf")

df3_all = vcf2pandas("examples/vcf3.vcf")

info = ["DP"]
samples = ["HG002"]
format_fields = ["GT", "AO"]
df3_selected = vcf2pandas("examples/vcf3.vcf")

To print to a text file:

with open("path_to_txt_file.txt") as f:
    f.write(df.to_string())