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vcfstats - powerful statistics for VCF files\n\n[![Pypi][1]][2] [![Github][3]][4] [![PythonVers][5]][2] [![docs][6]][13] ![github action][7] [![Codacy][9]][10] [![Codacy coverage][11]][10]\n\n[Documentation][13] | [CHANGELOG][12]\n\n## Motivation\n\nThere are a couple of tools that can plot some statistics of VCF files, including [`bcftools`][14] and [`jvarkit`][15]. However, none of them could:\n\n1. plot specific metrics\n2. customize the plots\n3. focus on variants with certain filters\n\nR package [`vcfR`][19] can do some of the above. However, it has to load entire VCF into memory, which is not friendly to large VCF files.\n\n## Installation\n\n```shell\npip install -U vcfstats\n```\n\nOr run with docker:\n\n```shell\ndocker run \\\n  -w /vcfstats/workdir \\\n  -v $(pwd):/vcfstats/workdir \\\n  --rm justold/vcfstats:latest \\\n  vcfstats \\\n  --vcf myfile.vcf \\\n  -o outputs \\\n  --formula 'COUNT(1) ~ CONTIG' \\\n  --title 'Number of variants on each chromosome'\n```\n\n## Gallery\n\n### Number of variants on each chromosome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1) ~ CONTIG' \\\n    --title 'Number of variants on each chromosome' \\\n    --config examples/config.toml\n```\n\n![Number of variants on each chromosome](examples/number-of-variants-on-each-chromosome.col.png)\n\n#### Changing labels and ticks\n\n`vcfstats` uses [`plotnine`][17] for plotting, read more about it on how to specify `--ggs` to modify the plots.\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1) ~ CONTIG' \\\n    --title 'Number of variants on each chromosome (modified)' \\\n    --config examples/config.toml \\\n    --ggs 'scale_x_discrete(name =\"Chromosome\", \\\n        limits=[\"1\",\"2\",\"3\",\"4\",\"5\",\"6\",\"7\",\"8\",\"9\",\"10\",\"X\"]); \\\n        ylab(\"# Variants\")'\n```\n\n![Number of variants on each chromosome (modified)](examples/number-of-variants-on-each-chromosome-modified.col.png)\n\n#### Number of variants on first 5 chromosome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1) ~ CONTIG[1,2,3,4,5]' \\\n    --title 'Number of variants on each chromosome (first 5)' \\\n    --config examples/config.toml\n# or\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1) ~ CONTIG[1-5]' \\\n    --title 'Number of variants on each chromosome (first 5)' \\\n    --config examples/config.toml\n# or\n# require vcf file to be tabix-indexed.\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1) ~ CONTIG' \\\n    --title 'Number of variants on each chromosome (first 5)' \\\n    --config examples/config.toml -r 1 2 3 4 5\n```\n\n![Number of variants on each chromosome (first 5)](examples/number-of-variants-on-each-chromosome-first-5.col.png)\n\n### Number of substitutions of SNPs\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1, VARTYPE[snp]) ~ SUBST[A\u003eT,A\u003eG,A\u003eC,T\u003eA,T\u003eG,T\u003eC,G\u003eA,G\u003eT,G\u003eC,C\u003eA,C\u003eT,C\u003eG]' \\\n    --title 'Number of substitutions of SNPs' \\\n    --config examples/config.toml\n```\n\n![Number of substitutions of SNPs](examples/number-of-substitutions-of-snps.col.png)\n\n#### Only with SNPs PASS all filters\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1, VARTYPE[snp]) ~ SUBST[A\u003eT,A\u003eG,A\u003eC,T\u003eA,T\u003eG,T\u003eC,G\u003eA,G\u003eT,G\u003eC,C\u003eA,C\u003eT,C\u003eG]' \\\n    --title 'Number of substitutions of SNPs (passed)' \\\n    --config examples/config.toml \\\n    --passed\n```\n\n![Number of substitutions of SNPs (passed)](examples/number-of-substitutions-of-snps-passed.col.png)\n\n### Alternative allele frequency on each chromosome\n\n```shell\n# using a dark theme\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'AAF ~ CONTIG' \\\n    --title 'Allele frequency on each chromosome' \\\n    --config examples/config.toml --ggs 'theme_dark()'\n```\n\n![Allele frequency on each chromosome](examples/allele-frequency-on-each-chromosome.violin.png)\n\n#### Using boxplot\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'AAF ~ CONTIG' \\\n    --title 'Allele frequency on each chromosome (boxplot)' \\\n    --config examples/config.toml \\\n    --figtype boxplot\n```\n\n![Allele frequency on each chromosome](examples/allele-frequency-on-each-chromosome-boxplot.boxplot.png)\n\n#### Using density plot/histogram to investigate the distribution:\n\nYou can plot the distribution, using density plot or histogram\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'AAF ~ CONTIG[1,2]' \\\n    --title 'Allele frequency on chromosome 1,2' \\\n    --config examples/config.toml \\\n    --figtype density\n```\n\n![Allele frequency on chromosome 1,2](examples/allele-frequency-on-chromosome-12.density.png)\n\n### Overall distribution of allele frequency\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'AAF ~ 1' \\\n    --title 'Overall allele frequency distribution' \\\n    --config examples/config.toml\n```\n\n![Overall allele frequency distribution](examples/overall-allele-frequency-distribution.histogram.png)\n\n#### Excluding some low/high frequency variants\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'AAF[0.05, 0.95] ~ 1' \\\n    --title 'Overall allele frequency distribution (0.05-0.95)' \\\n    --config examples/config.toml\n```\n\n![Overall allele frequency distribution](examples/overall-allele-frequency-distribution-0-05-0-95.histogram.png)\n\n### Counting types of variants on each chromosome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1, group=VARTYPE) ~ CHROM' \\\n    # or simply\n    # --formula 'VARTYPE ~ CHROM' \\\n    --title 'Types of variants on each chromosome' \\\n    --config examples/config.toml\n```\n\n![Types of variants on each chromosome](examples/types-of-variants-on-each-chromosome.col.png)\n\n#### Using bar chart if there is only one chromosome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'COUNT(1, group=VARTYPE) ~ CHROM[1]' \\\n    # or simply\n    # --formula 'VARTYPE ~ CHROM[1]' \\\n    --title 'Types of variants on chromosome 1' \\\n    --config examples/config.toml \\\n    --figtype pie\n```\n\n![Types of variants on chromosome 1](examples/types-of-variants-on-chromosome-1.pie.png)\n\n#### Counting variant types on whole genome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    # or simply\n    # --formula 'VARTYPE ~ 1' \\\n    --formula 'COUNT(1, group=VARTYPE) ~ 1' \\\n    --title 'Types of variants on whole genome' \\\n    --config examples/config.toml\n```\n\n![Types of variants on whole genome](examples/types-of-variants-on-whole-genome.col.png)\n\n### Counting type of mutant genotypes (HET, HOM_ALT) for sample 1 on each chromosome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    # or simply\n    # --formula 'GTTYPEs[HET,HOM_ALT]{0} ~ CHROM' \\\n    --formula 'COUNT(1, group=GTTYPEs[HET,HOM_ALT]{0}) ~ CHROM' \\\n    --title 'Mutant genotypes on each chromosome (sample 1)' \\\n    --config examples/config.toml\n```\n\n![Mutant genotypes on each chromosome](examples/mutant-genotypes-on-each-chromosome-sample-1.col.png)\n\n\n### Exploration of mean(genotype quality) and mean(depth) on each chromosome for sample 1\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'MEAN(GQs{0}) ~ MEAN(DEPTHs{0}, group=CHROM)' \\\n    --title 'GQ vs depth (sample 1)' \\\n    --config examples/config.toml\n```\n\n![GQ vs depth (sample 1)](examples/gq-vs-depth-sample-1.scatter.png)\n\n### Exploration of depths for sample 1,2\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n    --outdir examples/ \\\n    --formula 'DEPTHs{0} ~ DEPTHs{1}' \\\n    --title 'Depths between sample 1 and 2' \\\n    --config examples/config.toml\n```\n\n![Depths between sample 1 and 2](examples/depths-between-sample-1-and-2.scatter.png)\n\nSee more examples:\n\n[https://github.com/pwwang/vcfstats/issues/15#issuecomment-1029367903](https://github.com/pwwang/vcfstats/issues/15#issuecomment-1029367903)\n\n[1]: https://img.shields.io/pypi/v/vcfstats?style=flat-square\n[2]: https://pypi.org/project/vcfstats/\n[3]: https://img.shields.io/github/v/tag/pwwang/vcfstats?style=flat-square\n[4]: https://github.com/pwwang/vcfstats\n[5]: https://img.shields.io/pypi/pyversions/vcfstats?style=flat-square\n[6]: https://img.shields.io/github/actions/workflow/status/pwwang/vcfstats/docs.yml?label=docs\u0026style=flat-square\n[7]: https://img.shields.io/github/actions/workflow/status/pwwang/vcfstats/build.yml?style=flat-square\n[9]: https://img.shields.io/codacy/grade/c8c8bfa8c5e9443bbf268a0a7c6f206d?style=flat-square\n[10]: https://app.codacy.com/gh/pwwang/vcfstats/\n[11]: https://img.shields.io/codacy/coverage/c8c8bfa8c5e9443bbf268a0a7c6f206d?style=flat-square\n[12]: https://pwwang.github.io/vcfstats/CHANGELOG/\n[13]: https://pwwang.github.io/vcfstats/\n[14]: https://samtools.github.io/bcftools/bcftools.html#stats\n[15]: http://lindenb.github.io/jvarkit/VcfStatsJfx.html\n[17]: https://plotnine.readthedocs.io/en/stable/\n[19]: https://knausb.github.io/vcfR_documentation/visualization_1.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpwwang%2Fvcfstats","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpwwang%2Fvcfstats","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpwwang%2Fvcfstats/lists"}