Skip to content
This repository has been archived by the owner on Jul 2, 2020. It is now read-only.

Latest commit

 

History

History
32 lines (20 loc) · 1021 Bytes

README.md

File metadata and controls

32 lines (20 loc) · 1021 Bytes

vcf-sumstats

Usage:

java -jar vcf-sumstats.jar <number of cultivars> <command> [files]

Available commands:

  • VcfParser
  • Histograms
  • Linkage

Formats for each:

java -jar vcf-sumstats.jar <number of cultivars> VcfParser <folder containing VCFs> <output.tsv>

java -jar vcf-sumstats.jar <number of cultivars> Histograms <folder containing sorted variant TSVs> <annotatedRegions.tsv>

java -jar vcf-sumstats.jar <number of cultivars> Linkage <folder containing sorted SNP TSV>

Please use TSV files sorted alphabetically by scaffold and ascending by position!! This is very important!!!

A sample one liner would be: (head -n 2 <file> && tail -n +3 <file> | sort -k1,1 -k2,2n) > <sorted_file>

In this example, column 1 contains scaffold names (sorted alphabetically) and column 2. The header is excluded from sorting. If it's a variant file where the scaffold name and position are in one column, one could do this:

(head -n 2 <file> && tail -n +3 <file> | sort -k1,1 -k1,1n) > <sorted_file>