samtools/samtools_stats

statistics

counts

bam

sam

cram

Description

Reports alignment summary statistics for a BAM file.

Type

bash_script

License

MIT/Expat

Keywords

statistics

counts

bam

sam

cram

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

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

Inputs

Name	Type & Properties	Description
--input	file required	Input file.
--bai	file	Index file.
--fasta	file	Reference file the CRAM was created with.
--coverage -c	integer multiple	Coverage distribution min;max;step. Default: [1, 1000, 1].
--remove_dups -d	boolean_true	Exclude from statistics reads marked as duplicates.
--customized_index_file -X	boolean_true	Use a customized index file.
--required_flag -f	string	Required flag, 0 for unset. See also `samtools flags`. Default: `"0"`.
--filtering_flag -F	string	Filtering flag, 0 for unset. See also `samtools flags`. Default: `0`.
--GC_depth	double	The size of GC-depth bins (decreasing bin size increases memory requirement). Default: `20000`.
--insert_size -i	integer	Maximum insert size. Default: `8000`.
--id -I	string	Include only listed read group or sample name.
--read_length -l	integer	Include in the statistics only reads with the given read length. Default: `-1`.
--most_inserts -m	double	Report only the main part of inserts. Default: `0.99`.
--split_prefix -P	string	Path or string prefix for filepaths output by --split (default is input filename).
--trim_quality -q	integer	The BWA trimming parameter. Default: `0`.
--ref_seq -r	file	Reference sequence (required for GC-depth and mismatches-per-cycle calculation).
--split -S	string	Also write statistics to separate files split by tagged field.
--target_regions -t	file	Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.
--sparse -x	boolean_true	Suppress outputting IS rows where there are no insertions.
--remove_overlaps -p	boolean_true	Remove overlaps of paired-end reads from coverage and base count computations.
--cov_threshold -g	integer	Only bases with coverage above this value will be included in the target percentage computation. Default: `0`.
--input_fmt_option	string	Specify a single input file format option in the form of OPTION or OPTION=VALUE.
--reference	file	Reference sequence FASTA FILE.

Name

Type & Properties

--input

file

required

--bai

file

--fasta

file

--coverage

-c

integer

multiple

--remove_dups

-d

boolean_true

--customized_index_file

-X

boolean_true

--required_flag

-f

string

--filtering_flag

-F

string

--GC_depth

double

--insert_size

-i

integer

--id

-I

string

--read_length

-l

integer

--most_inserts

-m

double

--split_prefix

-P

string

--trim_quality

-q

integer

--ref_seq

-r

file

--split

-S

string

--target_regions

-t

file

--sparse

-x

boolean_true

--remove_overlaps

-p

boolean_true

--cov_threshold

-g

integer

--input_fmt_option

string

--reference

file

Outputs

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

Name

Type & Properties

--output

-o

file

required

output