vcf_to_dadi.py: VCF to dadi Conversion Function¶

Generates a dadi snp file from a vcf file.

The dadi snp file format is described in the dadi manual

https://dadi.readthedocs.io/en/latest/user-guide/importing-data/#snp-data-format

Gutenkunst RN, Hernandez RD, Williams SH, Bustamante CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5: e1000695. DOI: 10.1371/journal.pgen.1000695

Required Arguments¶

--vcf <input_vcf_filename>: The name of the vcf file. This can be a bgzipped vcf file. .
--model-file <model_file_name>: The name of a PPP model file.
--modelname <model_name>: The name of a model in the model file. The treemix file to be generated will contain the allele counts for each SNP in each of the populations. The treemix run will estimate the phylogeny for the populations in the model.
--out <output file name>: Specifies the complete output filename.

Optional Aguments¶

--bed-file <BED_file_name>

The BED file is a sorted UCSC-style bedfile containing chromosome locations of the SNPs to be included in the output files. The BED file has no header. The first column is the chromosome name (this must match the chromosome name in the vcf file). The second column is start position (0-based, open interval) The third column is end position (closed interval). Any other columns are ignored.

--outgroup_fasta <name of alternative reference sequence>

This option is used to specify the name of a fasta file to use as an alternative reference to that used for the vcf file.

This fasta file must have been properly aligned to the reference used in the vcf file.

This option can be useful, for example, if an ancestral or outgroup reference is available that more accurately identifies the ancestral (and thus derived) allele at each SNP than does the reference used to make the vcf file.

--comment <comment text>

Comment text to be included in the header of the output file.

Example usage¶

Example command-lines:

vcf_to_dadi.py -h

vcf_to_dadi.py --vcf  pan_example.vcf.gz --model-file  panmodels.model  --modelname 4Pop  --out vcf_dadisnp_bedfile_test.out  --comment testing bedfile --bed-file pan_example_regions.bed  

vcf_to_dadi.py --vcf  pan_example2.vcf.gz --model-file  panmodels.model  --modelname 4Pop --out  vcf_dadisnp_test.out  --comment testing comment  

vcf_to_dadi.py --vcf pan_example2.vcf.gz --model-file panmodels.model  --modelname 4Pop --out vcf_dadisnp_fasta_test.out  --comment testing outgroup-fasta --outgroup-fasta  chr22_pan_example2_ref.fa 