Usage Examples

Basic usage

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

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. This can be used to obtain 4-fold degenerate pi, 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

Site-level estimates

Note: site level estimates will be much slower to calculate than windowed estimates.

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