bcftools/bcftools_stats

Stats

VCF

BCF

Description

Parses VCF or BCF and produces a txt stats file which 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.

Type

bash_script

License

MIT/Expat, GNU

Keywords

Stats

VCF

BCF

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.0 \  
  -main-script target/nextflow/bcftools/bcftools_stats/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required multiple	Input VCF/BCF file. Maximum of two files.

Name

Type & Properties

--input

-i

file

required

multiple

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output txt statistics file.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--allele_frequency_bins --af_bins	string	Allele frequency bins, a list of bin values (0.1,0.5,1).
--allele_frequency_bins_file --af_bins_file	file	Same as allele_frequency_bins, but in a file. Format of file is one value per line. e.g. 0.1 0.5 1
--allele_frequency_tag --af_tag	string	Allele frequency tag to use, by default estimated from AN,AC or GT.
--first_allele_only --first_only	boolean_true	Include only 1st allele at multiallelic sites.
--collapse --c	string	Treat as identical records with <snps\|indels\|both\|all\|some\|none>. See https://samtools.github.io/bcftools/bcftools.html#common_options for details.
--depth --d	string	Depth distribution: min,max,bin size.
--exclude --e	string	Exclude sites for which the expression is true. See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
--exons --E	file	tab-delimited file with exons for indel frameshifts statistics. The columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz).
--apply_filters --f	string	Require at least one of the listed FILTER strings (e.g. "PASS,.").
--fasta_reference --F	file	Faidx indexed reference sequence file to determine INDEL context.
--include --i	string	Select sites for which the expression is true. See https://samtools.github.io/bcftools/bcftools.html#expressions for details.
--split_by_ID --I	boolean_true	Collect stats for sites with ID separately (known vs novel).
--regions --r	string	Restrict to comma-separated list of regions. Following formats are supported: chr\|chr:pos\|chr:beg-end\|chr:beg-[,…].
--regions_file --R	file	Restrict to regions listed in a file. Regions can be specified either on a VCF, BED, or tab-delimited file (the default). For more information check manual.
--regions_overlap	string	This option controls how overlapping records are determined: set to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); set to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, and includes indels with POS at the end of a region, which are technically outside the region); or set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-").
--samples --s	string	List of samples for sample stats, "-" to include all samples.
--samples_file --S	file	File of samples to include. e.g. sample1 1 sample2 2 sample3 2
--targets --t	string	Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF rather than using the tbi/csi index. Both -r and -t options can be applied simultaneously: -r uses the index to jump to a region and -t discards positions which are not in the targets. Unlike -r, targets can be prefixed with "^" to request logical complement. For example, "^X,Y,MT" indicates that sequences X, Y and MT should be skipped. Yet another difference between the -t/-T and -r/-R is that -r/-R checks for proper overlaps and considers both POS and the end position of an indel, while -t/-T considers the POS coordinate only (by default; see also --regions-overlap and --targets-overlap). Note that -t cannot be used in combination with -T. Following formats are supported: chr\|chr:pos\|chr:beg-end\|chr:beg-[,…].
--targets_file --T	file	Similar to --regions_file option but streams rather than index-jumps.
--targets_overlaps	string	Include if POS in the region (0), record overlaps (1), variant overlaps (2).
--user_tstv --u	string	Collect Ts/Tv stats for any tag using the given binning [0:1:100]. Format is <TAG[:min:max:n]>. A subfield can be selected as e.g. 'PV4[0]', here the first value of the PV4 tag.
--verbose --v	boolean_true	Produce verbose per-site and per-sample output.

Name

Type & Properties

--allele_frequency_bins

--af_bins

string

--allele_frequency_bins_file

--af_bins_file

file

--allele_frequency_tag

--af_tag

string

--first_allele_only

--first_only

boolean_true

--collapse

--c

string

--depth

--d

string

--exclude

--e

string

--exons

--E

file

--apply_filters

--f

string

--fasta_reference

--F

file

--include

--i

string

--split_by_ID

--I

boolean_true

--regions

--r

string

--regions_file

--R

file

--regions_overlap

string

--samples

--s

string

--samples_file

--S

file

--targets

--t

string

--targets_file

--T

file

--targets_overlaps

string

--user_tstv

--u

string

--verbose

--v

boolean_true