piawka

The powerful awk script to calculate π, Dxy (or πxy, or Nei's D) and some more simple stats (Fst, Tajima's D, Ronfort's rho) in VCF files in the command line. Developed to analyze arbitrary-ploidy groups with substantial amounts of missing data.

wiki

Install it!

Quickly: conda

conda install -c bioconda piawka

Quickly but slower

Make the following programs available in the command line (install and add to PATH):

• gawk v5.0.0 and above
• tabix

Then, get piawka by cloning the repo and add the scripts to PATH:

git clone https://github.com/novikovalab/piawka.git
export PATH="$( realpath ./piawka/scripts ):${PATH}"

Use it!

$ piawka
piawka v0.8.5
Usage:
piawka -g groups_tsv -v vcf_gz [OPTIONS]
Options:
-1, --persite       output values for each site
-a, --all           output more cols: numerator, denominator, nGeno, nMiss
-b, --bed <arg>     BED file with regions to be analyzed
-B, --targets <arg> BED file with targets (faster than -b for numerous small regions)
-D, --nodxy         do not output Dxy (and other pairwise metrics)
-f, --fst           output Hudson Fst
-F, --fstwc         output Weir and Cockerham Fst instead
-g, --groups <arg>  2-columns sample ID / group ID TSV file
-h, --help          show this help message
-H, --het           output only per-sample pi = heterozygosity
-j, --jobs <arg>    number of parallel jobs to run
-m, --mult          use multiallelic sites
-M, --miss          max share of missing GT per group at site
-P, --nopi          do not output pi values
-r, --rho           output Ronfort's rho
-t, --tajimalike    output Tajima's D-like stat (manages missing data but isn't a test)
-T, --tajima        output vanilla Tajima's D instead (sensitive to missing data)
-v, --vcf <arg>     gzipped and tabixed VCF file

See the wiki for further details.

Cite it!

If you want to express your gratitude for having piawka, please cite our Siberian Arabidopsis paper where we have introduced and first used it.