Parse VCF to dataframe using pyvcf (including format).

vcf_to_df.py

import vcf
import os
import pandas as pd
import matplotlib.pyplot as plt

def create_vcf_df(file_name):
    data = []
    csq_fields = ["impact", "aa.pos", "aa.mut", "nuc.pos", "codon.change"]
    vcf_reader = vcf.Reader(open("../data/"+file_name))
    for rec in vcf_reader:
        t = {}
        t["POS"] = rec.POS
        t["REF"] = rec.REF
        t["ALT"] = rec.ALT[0]   # Since VCF has only 1 ALT per position
        for k,v in rec.INFO.items():
            if k =="CSQ":
                for i,j in zip(v[0].split("|"), csq_fields):
                    if ".pos" in j:
                        i = int(i)
                    t["INFO.CSQ."+j] = i
            else:
                t["INFO."+k] = v
        for s in rec.samples:
            for f in rec.FORMAT.split(":"):
                t["s."+f] = s[f]
        t["file.name"] = file_name
        data.append(t)
    return pd.DataFrame(data)

files = os.listdir("../data")   # Concat list of files in all directories
dfs = [create_vcf_df(f) for f in files]

df = pd.concat(dfs)