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Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Brief description

This script takes as input a VCF file and will use the SNP genotypes to create a matrix for phylogenetic analysis in the PHYLIP (relaxed version), FASTA, NEXUS, or binary NEXUS formats. For heterozygous SNPs the consensus is made and the IUPAC nucleotide ambiguity codes are written to the final matrix(ces), any ploidy level is allowed and automatically detected. The code is optimized for large VCF matrices (hundreds of samples and millions of genotypes), for example, in our tests it processed a 20GB VCF (~3 million SNPs x 650 individuals) in ~27 minutes. The initial version of the script just produced a PHYLIP matrix but now we have added other popular formats, including the binary NEXUS file to run SNPs analysis with the SNAPP plugin in BEAST (only for diploid genotypes).

Additionally, you can choose a minimum number of samples per SNP to control the final amount of missing data. Since phylogenetic software usually root the trees at the first sequence in the alignment (e.g. RAxML, IQTREE, and MrBayes), the script also allows you to specify an OUTGROUP sequence that will be written in the first place in the alignment.

Compressed VCF files can be directly analyzed but the extension must be .vcf.gz.

The script has been tested with VCF files produced by pyrad v.3.0.66, ipyrad v.0.7.x, Stacks v.1.47, dDocent, GATK, freebayes, and graphtyper

Please don't hesitate to open an Issue if you find any problem or suggestions for a new feature.


Just type python -h to show the help of the program:

usage: [-h] -i FILENAME [--output-folder FOLDER]
                     [--output-prefix PREFIX] [-m MIN_SAMPLES_LOCUS]
                     [-o OUTGROUP] [-p] [-f] [-n] [-b] [-r] [-w] [-v]

The script converts a collection of SNPs in VCF format into a PHYLIP, FASTA,
NEXUS, or binary NEXUS file for phylogenetic analysis. The code is optimized
to process VCF files with sizes >1GB. For small VCF files the algorithm slows
down as the number of taxa increases (but is still fast).

Any ploidy is allowed, but binary NEXUS is produced only for diploid VCFs.

optional arguments:
  -h, --help            show this help message and exit
                        Name of the input VCF file, can be gzipped
  --output-folder FOLDER
                        Output folder name, it will be created if it does not
                        exist (same folder as input by default)
  --output-prefix PREFIX
                        Prefix for output filenames (same as the input VCF
                        filename without the extension by default)
  -m MIN_SAMPLES_LOCUS, --min-samples-locus MIN_SAMPLES_LOCUS
                        Minimum of samples required to be present at a locus
  -o OUTGROUP, --outgroup OUTGROUP
                        Name of the outgroup in the matrix. Sequence will be
                        written as first taxon in the alignment.
  -p, --phylip-disable  A PHYLIP matrix is written by default unless you
                        enable this flag
  -f, --fasta           Write a FASTA matrix (disabled by default)
  -n, --nexus           Write a NEXUS matrix (disabled by default)
  -b, --nexus-binary    Write a binary NEXUS matrix for analysis of biallelic
                        SNPs in SNAPP, only diploid genotypes will be
                        processed (disabled by default)
  -r, --resolve-IUPAC   Randomly resolve heterozygous genotypes to avoid IUPAC
                        ambiguities in the matrices (disabled by default)
  -w, --write-used-sites
                        Save the list of coordinates that passed the filters
                        and were used in the alignments (disabled by default)
  -v, --version         show program's version number and exit


In the following examples you can omit python if you change the permissions of to executable.

Example 1: Use default parameters to create a PHYLIP matrix with a minimum of 4 samples per SNP:

python --input myfile.vcf
# Which i equivalent to:
python -i myfile.vcf
# This command will create a PHYLIP called myfile_min4.phy

Example 2: Create a PHYLIP and a FASTA matrix using a minimum of 60 samples per SNP:

python --input myfile.vcf --fasta --min-samples-locus 60
# Which is equivalent to:
python -i myfile.vcf -f -m 60
# This command will create a PHYLIP called myfile_min60.phy and a FASTA called myfile_min60.fasta

Example 3: Create all output formats, and select "sample1" as outgroup:

python --input myfile.vcf --outgroup sample1 --fasta --nexus --nexus-binary
# Which is equivalent to:
python -i myfile.vcf -o sample1 -f -n -b
# This command will create a PHYLIP called myfile_min4.phy, a FASTA called myfile_min4.fasta, a NEXUS called, and a binary NEXUS called

Example 4: If, for example, you wish to disable the creation of the PHYLIP matrix and only create a NEXUS matrix:

python --input myfile.vcf --phylip-disable --nexus
# Which is equivalent to:
python -i myfile.vcf -p -n
# This command will create only a NEXUS matrix called

Example 5: If for some reason you don't want to have IUPAC ambiguities representing heterozygous genotypes:

python --input myfile.vcf --resolve-IUPAC
# Which is equivalent to:
python -i myfile.vcf -r
# This command will create only a PHYLIP matrix called myfile_min4.phy where IUPAC ambiguites have been randomly resolved

Example 6: Specify output folder and output prefix:

python -i myfile.vcf.gz --output-folder /data/results --output-prefix mymatrix
# This command will create the file `myfile.min4.phy` in the folder `/data/results`

Example 7: Write a list of the sites that were used in the alignments:

python -i myfile.vcf.gz -w
# This command will create the file `myfile.min4.phy` and the list `myfile.min4.used_sites.tsv`



Ortiz, E.M. 2019. vcf2phylip v2.0: convert a VCF matrix into several matrix formats for phylogenetic analysis. DOI:10.5281/zenodo.2540861

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