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Find-Variant-VCF-to-JSON

Introduction

We will parse a variant call format file. This file has one thousand variants in it. Each line after the header lines is a variant. We'll open the variant file and inspect its contents. We will parse each line and transform it into a JSON. The output will look something like this (I have shortened the output):

{ "ALT": "G", "CHROM": "4", "FILTER": "PASS", "ID": ".", "INFO": {

        "Gene.ensGene": "ENSG00000109471,ENSG00000138684",
        "Gene.refGene": "IL2,IL21",
        "GeneDetail.ensGene": "dist=38306,dist=117597",
        "GeneDetail.refGene": "dist=38536,dist=117597"
    },
    "POS": 123416186,
    "QUAL" :23.25,
    "REF": "A",
    "SAMPLE": {
        "XG102": {
            "AD": "51,8",
            "DP": "59",
            "GQ": "32",
            "GT": "0/1",
            "PL": "32,0,1388"
        }
}

This project has several small functions that will be used to generate the JSON above. Note that the method outlined is not necessarily optimal. It is just one way of parsing the file after breaking a large problem into small parts.

Note that the header which corresponds to the columns starts with one hash/pound (#) symbol. Skip all headers that start with two hashes/pounds (##).

Variant Call Format

The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project. Existing formats for genetic data such as General feature format (GFF) stored all of the genetic data, much of which is redundant because it will be shared across the genomes. By using the variant call format only the variations need to be stored along with a reference genome.

The VCF header

The header begins the file and provides metadata describing the body of the file. Header lines are denoted as starting with #. Special keywords in the header are denoted with ##. The header contains keywords that optionally semantically and syntactically describe the fields used in the body of the file, notably INFO, FILTER, and FORMAT

The columns of a VCF

CHROM The name of the sequence (typically a chromosome) on which the variation is being called. This sequence is usually known as 'the reference sequence', i.e. the sequence against which the given sample varies.

POS The 1-based position of the variation on the given sequence.

ID The identifier of the variation, e.g. a dbSNP rs identifier, or if unknown a ".". Multiple identifiers should be separated by semi-colons without white-space.

REF The reference base (or bases in the case of an indel) at the given position on the given reference sequence.

ALT The list of alternative alleles at this position.

QUAL A quality score associated with the inference of the given alleles.

FILTER A flag indicating which of a given set of filters the variation has passed.

INFO An extensible list of key-value pairs (fields) describing the variation. See below for some common fields. Multiple fields are separated by semicolons with optional values in the format: =[,data].

FORMAT An (optional) extensible list of fields for describing the samples. See below for some common fields.

SAMPLES For each (optional) sample described in the file, values are given for the fields listed in FORMAT

How script works?

The script has 12 steps with each step building a small function which will be used in the final step to generate the final output.

Input

A file containing 1000 variants. (lab1_data.vcf)

Output

  • A json file (lab1.json) containing the parsed variants into json.

  • A function which can take CHROM,REF,ALT ,POS and output_filename (containing all variants as json) as input and return a list of variants that match the given CHROM,REF,ALT and POS.