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.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/bcftools/bcftools_stats/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required multiple	Input VCF/BCF file(s). Maximum of two files can be provided. When two files are given, the program generates separate stats for intersection and the complements.

Name

Type & Properties

--input

file

required

multiple

Outputs

Name	Type & Properties	Description
--output -o	file required output	Write output to a file. The output is a text file which can be plotted using plot-vcfstats.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--af_bins	string	Allele frequency bins, a list of comma-separated bin values.
--af_tag	string	Allele frequency tag to use, by default estimated from AN,AC or GT.
--collapse -c	string	Treat as identical records with <snps\|indels\|both\|all\|some\|none>.
--depth -d	string	Depth distribution: min,max,bin size [0:200:1].
--exclude -e	string	Exclude sites for which the expression is true.
--exons -E	file	Tab-delimited file with exons for indel frameshifts statistics. The columns of the file are CHR, FROM, TO, with 1-based positions. The file should be BGZF-compressed and indexed with tabix.
--apply_filters -f	string	Require at least one of the listed FILTER strings.
--fasta_ref -F	file	Faidx indexed reference sequence file to determine INDEL context.
--first_allele_only --1st-allele-only	boolean_true	Include only 1st allele at multiallelic sites.
--include -i	string	Select sites for which the expression is true.
--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.
--regions_file -R	file	Restrict to regions listed in a file.
--regions_overlap	string	Include if POS in the region (pos), record overlaps (record), variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.
--samples -s	string	List of samples for sample stats, "-" to include all samples.
--samples_file -S	file	File of samples to include.
--targets -t	string	Similar to regions, but streams rather than using index. Targets can be prefixed with "^" for logical complement.
--targets_file -T	file	Similar to regions_file but streams rather than index-jumps.
--targets_overlap	string	Include if POS in the region (pos), record overlaps (record), variant overlaps (variant). Can also use numeric equivalents 0, 1, 2.
--user_tstv -u	string	Collect Ts/Tv stats for any tag using the given binning. Format is TAG[:min:max:n]. Default binning is [0:1:100].
--verbose -v	boolean_true	Produce verbose per-site and per-sample output.

Name

Type & Properties

--af_bins

string

--af_tag

string

--collapse

-c

string

--depth

-d

string

--exclude

-e

string

--exons

-E

file

--apply_filters

-f

string

--fasta_ref

-F

file

--first_allele_only

--1st-allele-only

boolean_true

--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_overlap

string

--user_tstv

-u

string

--verbose

-v

boolean_true