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VCF to PLINK Conversion

By Pavel Salazar-Fernandez ([email protected])

Human Population and Evolutionary Genomics Lab | LANGEBIO

About

Documentation: VCF [1000 Genomes]

This document explains how to manipulate VCF (Variant Call Format) files for their utilization in the PLINK software.

Concatenation

Documentation: bcftools concat

If the dataset is split in two or more VCF files (e.g. in chromosomes), it is necessary to concatenate them to create a single fused file. This procedure will create a compressed VCF file (.vcf.gz).

Program:

  • bcftools

Prerequisites:

  • All source files must have the same sample columns appearing in the same order.
  • Input files must be sorted by chromosome and positions.
  • Files must be given in the correct order.
  • (Optional) A file containing a ordered list of the input files

Command: bcftools concat -f [VCF files list] -o [Output file name] -O z

Output:

  • [FILE].vcf.tar.gz

Indexing

Documentation: tabix

If a VCF file is has no accompanying TBI file or was created by merging/concatenation, an index file must be created.

Program:

  • tabix

Prerequisites:

  • Input data file must be position sorted and compressed.

Command: tabix -p vcf [VCF file]

Output:

  • [FILE].vcf.tar.gz .tbi

Conversion

Reference: PLINK Documentation: VCF

Program:

  • plink (v1.9 or upper)

Requires:

  • VCF file and its index (.tbi)

Command:

plink --vcf [VCF File] \
	--keep-allele-order \
	--vcf-idspace-to _ \
	--const-fid \
	--autosome \
	--biallelic-only strict \
	--snps-only no-DI \
	--vcf-filter \
	--vcf-half-call m \
	--vcf-require-gt \
	--make-bed \
	--out [Output file name]

Flags:

  • --keep-allele-order: Maintains reference allele in the A2 position.
  • --vcf-idspace-to _: All ID spaces will be changed to "_" (recommended).
  • --const-fid: All samples will have the same FID (default '0').
  • --autosome: Only autosomal sites will be included.
  • --biallelic-only strict: Only biallelic sites present in samples will be included.
  • --snps-only no-DI: No deletions nor insertions.
  • --vcf-filter: Only calls that pass the quality filter will be included.
  • --vcf-half-call m: Set half-calls to missing.
  • --vcf-require-gt: Do not include sites with no genotype data.

Output:

  • [FILE].bed
  • [FILE].bim
  • [FILE].fam

Generating PED and MAP files

Program:

  • plink

Requires:

  • PLINK binary file set (BED, BIM & FAM files)

Command: plink --bfile [BED file] --recode --tab --out [Output file name]

Output:

  • [FILE].ped
  • [FILE].map

Note: PED file size may be considerably much bigger than its BED equivalent.

References

  1. Best practice for converting VCF files to plink format
  2. BCFtools
  3. PLINK Documentation