vcf_to_treemix.py: VCF to treemix Conversion Function¶

The treemix program was developed by Pickrell and Prichard (2012) to estimate phylogeny and admixture for closely related populations.

Pickrell JK, Pritchard JK (2012) Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. PLOS Genetics 8(11): e1002967.

The program can make use of very large numbers of SNPs.

vcf_to_treemix.py will generate a treemix input file from a vcf file.

If run using the --bed-file and --kblock options, the resulting treemix file can be run using the 'linkage disequilibrium' (-k) option. Under this option each block of kblock SNPs are treated as a linked group and different groups are treated as unlinked.

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 <outpuf_file_name>: The name of the treemix file to be generated. The file is bgzipped and '.gz' is added to the end of the name

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 file. 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.

If used with --kblock, each of the BED file regions is used to generate one block of SNPs

--kblock <k_block_size>

Used with --bed-file, for using treemix runtime option -k. k is the number of SNPs in a block in the treemix file. If the actual number of SNPs in a BED file interval is less than kblock, then additional invariant rows are added to the treemix file so the total numbers of rows for that and every block is equal to kblock. k is set to 1000 by default. It needs to be increased only when one or more BED file regions have more than k snps.

Example usage¶

Example command-lines:

vcf_to_treemix.py -h

   vcf_to_treemix.py --vcf pan_example.vcf.gz --model-file panmodels.model --modelname 4Pop --out vcf_treemixtest1 --bed-file pan_example_regions.bed --kblock 1000

.. code-block:: bash

   vcf_to_treemix.py --vcf pan_example.vcf.gz --model-file panmodels.model --modelname 4Pop --out vcf_treemixtest2    