Usage Examples

Basic usage

Compute π, F_ST, and d_xy in 10 kb windows across the whole VCF:

pixy --stats pi fst dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--window_size 10000 \
--n_cores 2

Including the new 2.0 statistics

Watterson's θ and Tajima's D are also computed in windows. They use the same populations file as π:

pixy --stats pi watterson_theta tajima_d \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--window_size 10000 \
--n_cores 4

Focusing on a specific genomic interval

pixy --stats pi fst dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--chromosomes 'X' \
--interval_start 15000 \
--interval_end 400000 \
--window_size 10000

Using a .BED file to define windows

When defined with a BED file, windows can be any size and non-uniform.

pixy --stats pi fst dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--bed_file genomic_windows.bed

Using a sites file to limit calculations to specific sites

Sites files define individual sites that will be included in the calculations. Useful for obtaining 4-fold degenerate π, or statistics for particular classes of genomic elements (genes, introns, etc.).

pixy --stats pi fst dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--sites_file valid_sites.txt

Including multiallelic SNPs

By default pixy considers only biallelic sites. Pass --include_multiallelic_snps to include sites with more than two alleles in the calculation (added in 2.0):

pixy --stats pi dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--window_size 10000 \
--include_multiallelic_snps

Switching the F_ST estimator

pixy defaults to Weir & Cockerham's F_ST. Pass --fst_type hudson to use the Hudson (1992) / Bhatia et al. (2013) estimator instead:

pixy --stats fst \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--window_size 10000 \
--fst_type hudson

Site-level estimates

Note

Site-level estimates are much slower to calculate than windowed estimates. Use --window_size 1 with a narrow interval for targeted lookups rather than genome-wide site-level scans.

pixy --stats pi fst dxy \
--vcf data/vcf/ag1000/chrX_36Ag_allsites.vcf.gz \
--populations Ag1000_sampleIDs_popfile.txt \
--window_size 1 \
--chromosomes 'X' \
--interval_start 15000 \
--interval_end 400000