{
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        "description": "# 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\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:\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```shell\npip install -U vcfstats\n```\n\nOr run with docker or singularity:\n```shell\ndocker run --rm justold/vcfstats:latest vcfstats\n# or\nsingularity run docker://justold/vcfstats:latest vcfstats\n```\n\n## Gallery\n\n### Number of variants on each chromosome\n\n```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'COUNT(1) ~ CONTIG' \\\n\t--title 'Number of variants on each chromosome' \\\n\t--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\t--outdir examples/ \\\n\t--formula 'COUNT(1) ~ CONTIG' \\\n\t--title 'Number of variants on each chromosome (modified)' \\\n\t--config examples/config.toml \\\n\t--ggs 'scale_x_discrete(name =\"Chromosome\", \\\n\t\tlimits=[\"1\",\"2\",\"3\",\"4\",\"5\",\"6\",\"7\",\"8\",\"9\",\"10\",\"X\"]); \\\n\t\tylab(\"# 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\t--outdir examples/ \\\n\t--formula 'COUNT(1) ~ CONTIG[1,2,3,4,5]' \\\n\t--title 'Number of variants on each chromosome (first 5)' \\\n\t--config examples/config.toml\n# or\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'COUNT(1) ~ CONTIG[1-5]' \\\n\t--title 'Number of variants on each chromosome (first 5)' \\\n\t--config examples/config.toml\n# or\n# require vcf file to be tabix-indexed.\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'COUNT(1) ~ CONTIG' \\\n\t--title 'Number of variants on each chromosome (first 5)' \\\n\t--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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--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]' \\\n\t--title 'Number of substitutions of SNPs' \\\n\t--config examples/config.toml\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\t--outdir examples/ \\\n\t--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]' \\\n\t--title 'Number of substitutions of SNPs (passed)' \\\n\t--config examples/config.toml \\\n\t--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```shell\n# using a dark theme\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'AAF ~ CONTIG' \\\n\t--title 'Allele frequency on each chromosome' \\\n\t--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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'AAF ~ CONTIG' \\\n\t--title 'Allele frequency on each chromosome (boxplot)' \\\n\t--config examples/config.toml \\\n\t--figtype boxplot\n```\n\n![Allele frequency on each chromosome](examples/allele-frequency-on-each-chromosome.boxplot.png)\n\n#### Using density plot/histogram to investigate the distribution:\nYou can plot the distribution, using density plot or histogram\n```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'AAF ~ CONTIG[1,2]' \\\n\t--title 'Allele frequency on chromosome 1,2' \\\n\t--config examples/config.toml \\\n\t--figtype density\n```\n![Allele frequency on chromosome 1,2](examples/allele-frequency-on-chromosome-1-2.density.png)\n\n### Overall distribution of allele frequency\n```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'AAF ~ 1' \\\n\t--title 'Overall allele frequency distribution' \\\n\t--config examples/config.toml\n```\n![Overall allele frequency distribution](examples/overall-allele-frequency-distribution.histogram.png)\n\n#### Excluding some low/high frequency variants\n```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'AAF[0.05, 0.95] ~ 1' \\\n\t--title 'Overall allele frequency distribution (0.05-0.95)' \\\n\t--config examples/config.toml\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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'COUNT(1, group=VARTYPE) ~ CHROM' \\\n\t# or simply\n\t# --formula 'VARTYPE ~ CHROM' \\\n\t--title 'Types of variants on each chromosome' \\\n\t--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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'COUNT(1, group=VARTYPE) ~ CHROM[1]' \\\n\t# or simply\n\t# --formula 'VARTYPE ~ CHROM[1]' \\\n\t--title 'Types of variants on chromosome 1' \\\n\t--config examples/config.toml \\\n\t--figtype pie\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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t# or simply\n\t# --formula 'VARTYPE ~ 1' \\\n\t--formula 'COUNT(1, group=VARTYPE) ~ 1' \\\n\t--title 'Types of variants on whole genome' \\\n\t--config examples/config.toml\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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t# or simply\n\t# --formula 'GTTYPEs[HET,HOM_ALT]{0} ~ CHROM' \\\n\t--formula 'COUNT(1, group=GTTYPEs[HET,HOM_ALT]{0}) ~ CHROM' \\\n\t--title 'Mutant genotypes on each chromosome (sample 1)' \\\n\t--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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'MEAN(GQs{0}) ~ MEAN(DEPTHs{0}, group=CHROM)' \\\n\t--title 'GQ vs depth (sample 1)' \\\n\t--config examples/config.toml\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```shell\nvcfstats --vcf examples/sample.vcf \\\n\t--outdir examples/ \\\n\t--formula 'DEPTHs{0} ~ DEPTHs{1}' \\\n\t--title 'Depths between sample 1 and 2' \\\n\t--config examples/config.toml\n```\n![Depths between sample 1 and 2](examples/depths-between-sample-1-and-2.scatter.png)\n\n\nSee more examples:\n\nhttps://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/workflow/status/pwwang/vcfstats/Build%20Docs?label=docs&style=flat-square\n[7]: https://img.shields.io/github/workflow/status/pwwang/vcfstats/Build%20and%20Deploy?style=flat-square\n[8]: https://travis-ci.org/pwwang/vcfstats\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[16]: https://www.r-project.org/\n[17]: https://plotnine.readthedocs.io/en/stable/\n[18]: https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html\n[19]: https://knausb.github.io/vcfR_documentation/visualization_1.html\n",
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