VCF_filter

A multi-threading versatile filter for VCF file, adapt especially for population genetic analysis.

Usage

--i [required]

input vcf/bcf file, gzipped accepted.

--o [required]

output vcf file.

--P [required]

a popMap file with two colums, corresponding to individual and population name, separated by tab, see popmap.txt.

--c

individual coverage for each population, can be a ratio (<=1) or number (>1).

--C

total genotyping rate for a site, can be a ratio (<=1) or number (>1).

--m

minimum depth for each individual genotype.

--M

maximum depth for a individual genotype.

--H

maximum observed heterozygosity (Ho) of each population.

--F

absolute maximum inbreeding coefficient (Fis) of each population.

--G

minimum Genotype quality (GQ).

--Q

minimum quality for each SNP (Q).

--g

global minor allele frequncy for a site.

--l

local minor allele frequncy, if a population has this many minor allele, evaluated by the given value, then retain this site.

--p

sites with a p-value below the threshold defined by this option are taken to be out of HWE, and therefore excluded.

--f

apply the filter (--H and --F) on each site instead of each population.

--T

number of threads.

--s

sort the final vcf file, recommond on.

--h

help message.

--totDP

total Depth range for each site, [min:max], e.g., 10:100 means the total depth for this site should between 10 and 100.

--avgDP

average Depth range for each site, [min:max], e.g., 10:100 means the average depth for this site should between 10 and 100.

--reNb

retain non-bi-allelic sites, default unset.

--reMo

retain monomorphic sites, default unset.

--reIn

retain indels, defalt unset.

--rePo

threshold to define a polymorphic loci of each populations, should be a ratio.

Example usage

VCF_filter_multi.pl --i samples.vcf.gz --P popmap.txt --o qc.vcf.gz --c 0.8 --C 0.9 --m 6 --H 0.75 --G 20 --Q 20 --g 0.05 --l 0.2 --p 0.01 --avgDP 6:20 --T 8 --s --f

Which set:
at least 80% individuals of each population cover this site
at least 90% individuals totally cover this site
minimum read depth of 6
maximum observed heterozygosity considering all individuals (as --f set) <=0.75
genotyping quality >=20
snp quality >=20
minor allele frequency >=5%
retain a site if one population with minor allele frequency >=20%
exclude a site if p-value of HWE test <=0.01
average read depth for a site should between 6 and 20
use 8 cpus
sort the final vcf