vcfstats - powerful statistics for VCF files

Documentation | CHANGELOG

Motivation

There are a couple of tools that can plot some statistics of VCF files, including bcftools and jvarkit. However, none of them could:

1. plot specific metrics
2. customize the plots
3. focus on variants with certain filters

R package vcfR can do some of the above. However, it has to load entire VCF into memory, which is not friendly to large VCF files.

Installation

shell pip install -U vcfstats

Or run with docker:

shell docker run \ -w /vcfstats/workdir \ -v $(pwd):/vcfstats/workdir \ --rm justold/vcfstats:latest \ vcfstats \ --vcf myfile.vcf \ -o outputs \ --formula 'COUNT(1) ~ CONTIG' \ --title 'Number of variants on each chromosome'

Gallery

Number of variants on each chromosome

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1) ~ CONTIG' \ --title 'Number of variants on each chromosome' \ --config examples/config.toml

Changing labels and ticks

vcfstats uses plotnine for plotting, read more about it on how to specify --ggs to modify the plots.

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1) ~ CONTIG' \ --title 'Number of variants on each chromosome (modified)' \ --config examples/config.toml \ --ggs 'scale_x_discrete(name ="Chromosome", \ limits=["1","2","3","4","5","6","7","8","9","10","X"]); \ ylab("# Variants")'

Number of variants on first 5 chromosome

```shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1) ~ CONTIG[1,2,3,4,5]' \ --title 'Number of variants on each chromosome (first 5)' \ --config examples/config.toml

or

vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1) ~ CONTIG[1-5]' \ --title 'Number of variants on each chromosome (first 5)' \ --config examples/config.toml

or

require vcf file to be tabix-indexed.

vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1) ~ CONTIG' \ --title 'Number of variants on each chromosome (first 5)' \ --config examples/config.toml -r 1 2 3 4 5 ```

Number of substitutions of SNPs

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1, VARTYPE[snp]) ~ SUBST[A>T,A>G,A>C,T>A,T>G,T>C,G>A,G>T,G>C,C>A,C>T,C>G]' \ --title 'Number of substitutions of SNPs' \ --config examples/config.toml

Only with SNPs PASS all filters

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1, VARTYPE[snp]) ~ SUBST[A>T,A>G,A>C,T>A,T>G,T>C,G>A,G>T,G>C,C>A,C>T,C>G]' \ --title 'Number of substitutions of SNPs (passed)' \ --config examples/config.toml \ --passed

Alternative allele frequency on each chromosome

```shell

using a dark theme

vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'AAF ~ CONTIG' \ --title 'Allele frequency on each chromosome' \ --config examples/config.toml --ggs 'theme_dark()' ```

Using boxplot

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'AAF ~ CONTIG' \ --title 'Allele frequency on each chromosome (boxplot)' \ --config examples/config.toml \ --figtype boxplot

Using density plot/histogram to investigate the distribution:

You can plot the distribution, using density plot or histogram

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'AAF ~ CONTIG[1,2]' \ --title 'Allele frequency on chromosome 1,2' \ --config examples/config.toml \ --figtype density

Overall distribution of allele frequency

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'AAF ~ 1' \ --title 'Overall allele frequency distribution' \ --config examples/config.toml

Excluding some low/high frequency variants

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'AAF[0.05, 0.95] ~ 1' \ --title 'Overall allele frequency distribution (0.05-0.95)' \ --config examples/config.toml

Counting types of variants on each chromosome

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1, group=VARTYPE) ~ CHROM' \ # or simply # --formula 'VARTYPE ~ CHROM' \ --title 'Types of variants on each chromosome' \ --config examples/config.toml

Using bar chart if there is only one chromosome

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'COUNT(1, group=VARTYPE) ~ CHROM[1]' \ # or simply # --formula 'VARTYPE ~ CHROM[1]' \ --title 'Types of variants on chromosome 1' \ --config examples/config.toml \ --figtype pie

Counting variant types on whole genome

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ # or simply # --formula 'VARTYPE ~ 1' \ --formula 'COUNT(1, group=VARTYPE) ~ 1' \ --title 'Types of variants on whole genome' \ --config examples/config.toml

Counting type of mutant genotypes (HET, HOM_ALT) for sample 1 on each chromosome

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ # or simply # --formula 'GTTYPEs[HET,HOM_ALT]{0} ~ CHROM' \ --formula 'COUNT(1, group=GTTYPEs[HET,HOM_ALT]{0}) ~ CHROM' \ --title 'Mutant genotypes on each chromosome (sample 1)' \ --config examples/config.toml

Exploration of mean(genotype quality) and mean(depth) on each chromosome for sample 1

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'MEAN(GQs{0}) ~ MEAN(DEPTHs{0}, group=CHROM)' \ --title 'GQ vs depth (sample 1)' \ --config examples/config.toml

Exploration of depths for sample 1,2

shell vcfstats --vcf examples/sample.vcf \ --outdir examples/ \ --formula 'DEPTHs{0} ~ DEPTHs{1}' \ --title 'Depths between sample 1 and 2' \ --config examples/config.toml

See more examples:

https://github.com/pwwang/vcfstats/issues/15#issuecomment-1029367903