run-examples.sh

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

if [ $? -ne 0 ]; then exit 1; fi

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")'

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi

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

if [ $? -ne 0 ]; then exit 1; fi