VERSION

This manual page was last updated 2018-03-31 and refers to bcftools git version 1.8.

BCF1

The BCF1 format output by versions of samtools <= 0.1.19 is not compatible with this version of bcftools. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0.1.19 to convert to VCF, which can then be read by this version of bcftools.

    samtools-0.1.19/bcftools/bcftools view file.bcf1 | bcftools view

VARIANT CALLING

See bcftools call for variant calling from the output of the samtools mpileup command. In versions of samtools <= 0.1.19 calling was done with bcftools view. Users are now required to choose between the old samtools calling model (-c/--consensus-caller) and the new multiallelic calling model (-m/--multiallelic-caller). The multiallelic calling model is recommended for most tasks.

Common Options

The following options are common to many bcftools commands. See usage for specific commands to see if they apply.

    bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n

    sample1    1
    sample2    2
    sample3    2

  or

    sample1    M
    sample2    F
    sample3    F

  or a .ped file (here is shown a minimum working example, the first column is
  ignored and the last indicates sex: 1=male, 2=female)

    ignored daughterA fatherA motherA 2
    ignored sonB fatherB motherB 1

    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz

bcftools annotate [OPTIONS] FILE

Add or remove annotations.

    # Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
    1  752566  SomeString      5
    1  798959  SomeOtherString 6
    # etc.

    ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
    ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">

    bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf

Examples:

    # Remove three fields
    bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz

    # Remove all INFO fields and all FORMAT fields except for GT and PL
    bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf

    # Add ID, QUAL and INFO/TAG, not replacing TAG if already present
    bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf

    # Carry over all INFO and FORMAT annotations except FORMAT/GT
    bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf

    # Annotate from a tab-delimited file with six columns (the fifth is ignored),
    # first indexing with tabix. The coordinates are 1-based.
    tabix -s1 -b2 -e2 annots.tab.gz
    bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf

    # Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
    tabix -s1 -b2 -e3 annots.tab.gz
    bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf

    # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
    bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf

bcftools call [OPTIONS] FILE

This command replaces the former bcftools view caller. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option.

    X 1 60000 M 1
    X 2699521 154931043 M 1
    Y 1 59373566 M 1
    Y 1 59373566 F 0
    MT 1 16569 M 1
    MT 1 16569 F 1
    *  * *     M 2
    *  * *     F 2

    # Extract AN,AC values from an existing VCF, such 1000Genomes
    bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz

    # If the tags AN,AC are not already present, use the +fill-AN-AC plugin
    bcftools +fill-AN-AC 1000Genomes.bcf | bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' | bgzip -c > AFs.tab.gz
    tabix -s1 -b2 -e2 AFs.tab.gz

    # Create a VCF header description, here we name the tags REF_AN,REF_AC
    cat AFs.hdr
    ##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes">
    ##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele">

    # Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
    bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]

bcftools cnv [OPTIONS] FILE

Copy number variation caller, requires a VCF annotated with the Illumina’s B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM considers the following copy number states: CN 2 (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain).

bcftools concat [OPTIONS] FILE1 FILE2 […]

Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. Can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, --allow-overlaps option is specified. With the --naive option, the files are concatenated without being recompressed, which is very fast but dangerous if the BCF headers differ.

bcftools consensus [OPTIONS] FILE

Create consensus sequence by applying VCF variants to a reference fasta file. By default, the program will apply all ALT variants to the reference fasta to obtain the consensus sequence. Using the --sample (and, optionally, --haplotype) option will apply genotype (haplotype) calls from FORMAT/GT. Note that the program does not act as a primitive variant caller and ignores allelic depth information, such as INFO/AD or FORMAT/AD. For that, consider using the setGT plugin.

Examples:

    # Apply variants present in sample "NA001", output IUPAC codes for hets
    bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa

    # Create consensus for one region. The fasta header lines are then expected
    # in the form ">chr:from-to".
    samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa

bcftools convert [OPTIONS] FILE

  .gen
  ----
  1:111485207_G_A 1:111485207_G_A 111485207 G A 0 1 0 0 1 0
  1:111494194_C_T 1:111494194_C_T 111494194 C T 0 1 0 0 0 1

  .sample
  -------
  ID_1 ID_2 missing
  0 0 0
  sample1 sample1 0
  sample2 sample2 0

    MaleSample    M
    FemaleSample  F

  .hap
  ----
  1:111485207_G_A rsID1 111485207 G A 0 1 0 0
  1:111494194_C_T rsID2 111494194 C T 0 1 0 0
  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0

    MaleSample    M
    FemaleSample  F

  .hap
  -----
  0 1 0 0 1 0
  0 1 0 0 0 1

  .legend
  -------
  id position a0 a1
  1:111485207_G_A 111485207 G A
  1:111494194_C_T 111494194 C T

  .sample
  -------
  sample population group sex
  sample1 sample1 sample1 2
  sample2 sample2 sample2 2

    MaleSample    M
    FemaleSample  F

# Convert 23andme results into VCF
bcftools convert -c ID,CHROM,POS,AA -s SampleName -f 23andme-ref.fa --tsv2vcf 23andme.txt -Oz -o out.vcf.gz

bcftools csq [OPTIONS] FILE

Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby frame-shifting indels which in combination in fact are not frame-shifting.

The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option). The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask. The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags. By default this is 16, but if more are required, see the --ncsq option.

The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.

By default, the input VCF should be phased. If phase is unknown, or only partially known, the --phase option can be used to indicate how to handle unphased data. Alternatively, haplotype aware calling can be turned off with the --local-csq option.

If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis.

Symbolic alleles are not supported. They will remain unannotated in the output VCF and are ignored for the prediction analysis.

    # The program looks for "CDS", "exon", "three_prime_UTR" and "five_prime_UTR" lines,
    # looks up their parent transcript (determined from the "Parent=transcript:" attribute),
    # the gene (determined from the transcript's "Parent=gene:" attribute), and the biotype
    # (the most interesting is "protein_coding").
    #
    # Attributes required for
    #   gene lines:
    #   - ID=gene:<gene_id>
    #   - biotype=<biotype>
    #   - Name=<gene_name>      [optional]
    #
    #   transcript lines:
    #   - ID=transcript:<transcript_id>
    #   - Parent=gene:<gene_id>
    #   - biotype=<biotype>
    #
    #   other lines (CDS, exon, five_prime_UTR, three_prime_UTR):
    #   - Parent=transcript:<transcript_id>
    #
    # Supported biotypes:
    #   - see the function gff_parse_biotype() in bcftools/csq.c

    1   ignored_field  gene            21  2148  .   -   .   ID=gene:GeneId;biotype=protein_coding;Name=GeneName
    1   ignored_field  transcript      21  2148  .   -   .   ID=transcript:TranscriptId;Parent=gene:GeneId;biotype=protein_coding
    1   ignored_field  three_prime_UTR 21  2054  .   -   .   Parent=transcript:TranscriptId
    1   ignored_field  exon            21  2148  .   -   .   Parent=transcript:TranscriptId
    1   ignored_field  CDS             21  2148  .   -   1   Parent=transcript:TranscriptId
    1   ignored_field  five_prime_UTR  210 2148  .   -   .   Parent=transcript:TranscriptId

Examples:

    # Basic usage
    bcftools csq -f hs37d5.fa -g Homo_sapiens.GRCh37.82.gff3.gz in.vcf -Ob -o out.bcf

    # Extract the translated haplotype consequences. The following TBCSQ variations
    # are recognised:
    #   %TBCSQ    .. print consequences in all haplotypes in separate columns
    #   %TBCSQ{0} .. print the first haplotype only
    #   %TBCSQ{1} .. print the second haplotype only
    #   %TBCSQ{*} .. print a list of unique consquences present in either haplotype
    bcftools query -f'[%CHROM\t%POS\t%SAMPLE\t%TBCSQ\n]' out.bcf

Examples of BCSQ annotation:

    # Two separate VCF records at positions 2:122106101 and 2:122106102
    # change the same codon. This UV-induced C>T dinucleotide mutation
    # has been annotated fully at the position 2:122106101 with
    #   - consequence type
    #   - gene name
    #   - ensembl transcript ID
    #   - coding strand (+ fwd, - rev)
    #   - amino acid position (in the coding strand orientation)
    #   - list of corresponding VCF variants
    # The annotation at the second position gives the position of the full
    # annotation
    BCSQ=missense|CLASP1|ENST00000545861|-|1174P>1174L|122106101G>A+122106102G>A
    BCSQ=@122106101

    # A frame-restoring combination of two frameshift insertions C>CG and T>TGG
    BCSQ=@46115084
    BCSQ=inframe_insertion|COPZ2|ENST00000006101|-|18AGRGP>18AQAGGP|46115072C>CG+46115084T>TGG

    # Stop gained variant
    BCSQ=stop_gained|C2orf83|ENST00000264387|-|141W>141*|228476140C>T

    # The consequence type of a variant downstream from a stop are prefixed with *
    BCSQ=*missense|PER3|ENST00000361923|+|1028M>1028T|7890117T>C

bcftools filter [OPTIONS] FILE

Apply fixed-threshold filters.

The SNPs at positions 1 and 7 are filtered, positions 0 and 8 are not:
         0123456789
    ref  .G.GT..G..
    del  .A.G-..A..
Here the positions 1 and 6 are filtered, 0 and 7 are not:
         0123-456789
    ref  .G.G-..G..
    ins  .A.GT..A..

The second indel is filtered:
         012345678901
    ref  .GT.GT..GT..
    del  .G-.G-..G-..
And similarly here, the second is filtered:
         01 23 456 78
    ref  .A-.A-..A-..
    ins  .AT.AT..AT..

bcftools gtcheck [OPTIONS] [-g genotypes.vcf.gz] query.vcf.gz

Checks sample identity. The program can operate in two modes. If the -g option is given, the identity of the -s sample from query.vcf.gz is checked against the samples in the -g file. Without the -g option, multi-sample cross-check of samples in query.vcf.gz is performed.

        \sum_s { min_G { PL_a(G) + PL_b(G) } },

bcftools index [OPTIONS] in.bcf|in.vcf.gz

Creates index for bgzip compressed VCF/BCF files for random access. CSI (coordinate-sorted index) is created by default. The CSI format supports indexing of chromosomes up to length 2^31. TBI (tabix index) index files, which support chromosome lengths up to 2^29, can be created by using the -t/--tbi option or using the tabix program packaged with htslib. When loading an index file, bcftools will try the CSI first and then the TBI.

bcftools isec [OPTIONS] A.vcf.gz B.vcf.gz […]

Creates intersections, unions and complements of VCF files. Depending on the options, the program can output records from one (or more) files which have (or do not have) corresponding records with the same position in the other files.

    bcftools isec -p dir A.vcf.gz B.vcf.gz

    bcftools isec -e'MAF<0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir

    bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz

    bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz

    bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz

bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz […]

Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file. For example, when merging file A.vcf.gz containing samples S1, S2 and S3 and file B.vcf.gz containing samples S3 and S4, the output file will contain four samples named S1, S2, S3, 2:S3 and S4.

Note that it is responsibility of the user to ensure that the sample names are unique across all files. If they are not, the program will exit with an error unless the option --force-samples is given. The sample names can be also given explicitly using the --print-header and --use-header options.

Note that only records from different files can be merged, never from the same file. For "vertical" merge take a look at bcftools norm instead.

-m none   ..  no new multiallelics, output multiple records instead
-m snps   ..  allow multiallelic SNP records
-m indels ..  allow multiallelic indel records
-m both   ..  both SNP and indel records can be multiallelic
-m all    ..  SNP records can be merged with indel records
-m id     ..  merge by ID

bcftools mpileup [OPTIONS] -f ref.fa in.bam [in2.bam […]]

Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files. This is based on the original samtools mpileup command (with the -v or -g options) producing genotype likelihoods in VCF or BCF format, but not the textual pileup output. The mpileup command was transferred to bcftools in order to avoid errors resulting from use of incompatible versions of samtools and bcftools when using in the mpileup+bcftools call pipeline.

Individuals are identified from the SM tags in the @RG header lines. Multiple individuals can be pooled in one alignment file, also one individual can be separated into multiple files. If sample identifiers are absent, each input file is regarded as one sample.

Note that there are two orthogonal ways to specify locations in the input file; via -r region and -t positions. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index. The two may be used in conjunction. For example a BED file containing locations of genes in chromosome 20 could be specified using -r 20 -t chr20.bed, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the BED file. Also note that the -r option can be much slower than -t with many regions and can require more memory when multiple regions and many alignment files are processed.

    RG_ID_1
    RG_ID_2  SAMPLE_A
    RG_ID_3  SAMPLE_A
    RG_ID_4  SAMPLE_B
    RG_ID_5  FILE_1.bam  SAMPLE_A
    RG_ID_6  FILE_2.bam  SAMPLE_A
    *        FILE_3.bam  SAMPLE_C
    ?        FILE_3.bam  SAMPLE_D

    bcftools mpileup -Ou -f ref.fa aln.bam | \
    bcftools call -Ou -mv | \
    bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf

bcftools norm [OPTIONS] file.vcf.gz

Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. Left-alignment and normalization will only be applied if the --fasta-ref option is supplied.

bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]

A common framework for various utilities. The plugins can be used the same way as normal commands only their name is prefixed with "+". Most plugins accept two types of parameters: general options shared by all plugins followed by a separator, and a list of plugin-specific options. There are some exceptions to this rule, some plugins do not accept the common options and implement their own parameters. Therefore please pay attention to the usage examples that each plugin comes with.

# List options common to all plugins
bcftools plugin

# List available plugins
bcftools plugin -l

# Run a plugin
bcftools plugin counts in.vcf

# Run a plugin using the abbreviated "+" notation
bcftools +counts in.vcf

# The input VCF can be streamed just like in other commands
cat in.vcf | bcftools +counts

# Print usage information of plugin "dosage"
bcftools +dosage -h

# Replace missing genotypes with 0/0
bcftools +missing2ref in.vcf

# Replace missing genotypes with 0|0
bcftools +missing2ref in.vcf -- -p

// Short description used by 'bcftools plugin -l'
const char *about(void);

// Longer description used by 'bcftools +name -h'
const char *usage(void);

// Called once at startup, allows initialization of local variables.
// Return 1 to suppress normal VCF/BCF header output, -1 on critical
// errors, 0 otherwise.
int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);

// Called for each VCF record, return NULL to suppress the output
bcf1_t *process(bcf1_t *rec);

// Called after all lines have been processed to clean up
void destroy(void);

bcftools polysomy [OPTIONS] file.vcf.gz

Detect number of chromosomal copies in VCFs annotates with the Illumina’s B-allele frequency (BAF) values. Note that this command is not compiled in by default, see the section Optional Compilation with GSL in the INSTALL file for help.

bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]

Extracts fields from VCF or BCF files and outputs them in user-defined format.

%CHROM          The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
%INFO/TAG       Any tag in the INFO column
%TYPE           Variant type (REF, SNP, MNP, INDEL, BND, OTHER)
%MASK           Indicates presence of the site in other files (with multiple files)
%TAG{INT}       Curly brackets to subscript vectors (0-based)
%FIRST_ALT      Alias for %ALT{0}
[]              Format fields must be enclosed in brackets to loop over all samples
%GT             Genotype (e.g. 0/1)
%TBCSQ          Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
%TGT            Translated genotype (e.g. C/A)
%IUPACGT        Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
%LINE           Prints the whole line
%SAMPLE         Sample name
%POS0           POS in 0-based coordinates
%END            End position of the REF allele
%END0           End position of the REF allele in 0-based cordinates
\n              new line
\t              tab character

Everything else is printed verbatim.

# Print chromosome, position, ref allele and the first alternate allele
bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz

# Similar to above, but use tabs instead of spaces, add sample name and genotype
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz

# Print FORMAT/GT fields followed by FORMAT/GT fields
bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf

# Make a BED file: chr, pos (0-based), end pos (1-based), id
bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf

# Print only samples with alternate (non-reference) genotypes
bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf

# Print all samples at sites with at least one alternate genotype
bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

bcftools reheader [OPTIONS] file.vcf.gz

Modify header of VCF/BCF files, change sample names.

bcftools roh [OPTIONS] file.vcf.gz

A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.

Notation:
  D  = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity),
  f  = non-ref allele frequency

Emission probabilities:
  oAZ = P_i(D|AZ) = (1-f)*P(D|RR) + f*P(D|AA)
  oHW = P_i(D|HW) = (1-f)^2 * P(D|RR) + f^2 * P(D|AA) + 2*f*(1-f)*P(D|RA)

Transition probabilities:
  tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
  tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter

  ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
  AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
  HWi = P_i(HW)

  P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]

    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\t%INFO/TAG\n' file.vcf | bgzip -c > freqs.tab.gz

bcftools sort [OPTIONS] file.bcf

bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]

Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats. When two files are given, the program generates separate stats for intersection and the complements. By default only sites are compared, -s/-S must given to include also sample columns. When one VCF file is specified on the command line, then stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are given, then stats such as concordance (Genotype concordance by non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode.

    tabix -s1 -b2 -e3 file.gz

bcftools view [OPTIONS] file.vcf.gz [REGION […]]

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF. Former bcftools subset.

bcftools help [COMMAND] | bcftools --help [COMMAND]

Display a brief usage message listing the bcftools commands available. If the name of a command is also given, e.g., bcftools help view, the detailed usage message for that particular command is displayed.

bcftools [--version|-v]

Display the version numbers and copyright information for bcftools and the important libraries used by bcftools.

bcftools [--version-only]

Display the full bcftools version number in a machine-readable format.

plot-vcfstats [OPTIONS] file.vchk […]

Script for processing output of bcftools stats. It can merge results from multiple outputs (useful when running the stats for each chromosome separately), plots graphs and creates a PDF presentation.