gatk4/gatk4_markduplicates

deduplication

alignment

BAM

GATK

GATK4

Picard

Description

Identifies duplicate reads in a SAM/BAM/CRAM file.

This tool locates and tags duplicate reads in a coordinate-sorted SAM,
BAM or CRAM file, where duplicate reads are defined as originating from
a single fragment of DNA. Duplicates can arise during sample preparation
(e.g. library construction using PCR) or from a single amplification
cluster incorrectly detected as multiple clusters by the optical sensor
of the sequencing instrument (optical duplicates).

The tool works by comparing sequences in the 5' positions of both reads
and read-pairs. After duplicate reads are collected, the tool
differentiates the primary and duplicate reads using an algorithm that
ranks reads by the sums of their base-quality scores by default.
Duplicate reads are marked with the hexadecimal SAM flag value 0x0400
(decimal 1024).

In addition to the dedup-tagged output file, the tool produces a metrics
file indicating the numbers of duplicates for both single- and
paired-end reads.

Type

bash_script

License

Apache-2.0

Keywords

deduplication

alignment

BAM

GATK

GATK4

Picard

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/gatk4/gatk4_markduplicates/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input -I	file required multiple	Input coordinate-sorted SAM, BAM or CRAM file(s) to analyze. Can be specified multiple times to merge and de-duplicate reads across several input files in a single pass.

Name

Type & Properties

--input

-I

file

required

multiple

Output

Name	Type & Properties	Description
--output -O	file required output	Output file with duplicate reads marked (or removed, see `--remove_duplicates`).
--metrics -M	file required output	Output metrics file with duplication metrics, including the estimated library size.

Name

Type & Properties

--output

-O

file

required

output

--metrics

-M

file

required

output

Options

Name	Type & Properties	Description
--add_pg_tag_to_reads	boolean	Add a `PG` tag to each read in a SAM or BAM file. Default: true.
--assume_sort_order -ASO	string	If provided, assume that the input file has this sort order even if the header says otherwise.
--barcode_tag	string	Barcode SAM tag (e.g. `BC` for 10x Genomics) used to facilitate duplicate marking using molecular barcodes.
--clear_dt	boolean	Clear the `DT` tag from input SAM records. Should be set to `false` if the input SAM file doesn't have this tag. Default: true.
--comment -CO	string multiple	Comment(s) to include in the output file's header. May be specified more than once.
--create_index	boolean_true	If set, create an index when writing a coordinate-sorted BAM output file.
--duplex_umi	boolean_true	Treat UMIs as being duplex stranded. This option requires that the UMI consist of two equal-length strings separated by a hyphen (e.g. `ATC-GTC`). Reads are considered duplicates if, in addition to the standard definition, they have identical normalized UMIs. Requires `--barcode_tag` to hold non-normalized UMIs.
--duplicate_scoring_strategy -DS	string	The scoring strategy for choosing the non-duplicate among duplicate candidates. Default: 'SUM_OF_BASE_QUALITIES'.
--max_file_handles_for_read_ends_map -MAX_FILE_HANDLES	integer	Maximum number of file handles to keep open when spilling read ends to disk. Set this number a little lower than the per-process maximum number of files that may be open (find this with the `ulimit -n` command on a Unix system). Default: 8000.
--max_optical_duplicate_set_size	long	The maximum size of a set of duplicate reads for which to attempt to determine which are optical duplicates. Raising this value too high for a very large set of duplicate reads will severely affect the runtime of this tool. Set to `-1` to completely disable this check. Default: 300000.
--max_records_in_ram	integer	When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. Default: 500000.
--molecular_identifier_tag	string	SAM tag used to uniquely identify the molecule from which a read was derived. Requires `--barcode_tag` to also be set.
--optical_duplicate_pixel_distance	integer	The maximum offset between two duplicate clusters in order to consider them optical duplicates. A value of `100` is appropriate for non-patterned flowcells. For patterned flowcell models (e.g. NovaSeq, HiSeqX), `2500` is more appropriate. For other platforms and models, experiment to find what works best. Default: 100.
--program_group_command_line -PG_COMMAND	string	Value of the `CL` tag of the `PG` record to be created. If not supplied, the command line is detected automatically.
--program_group_name -PG_NAME	string	Value of the `PN` tag of the `PG` record to be created. Default: 'MarkDuplicates'.
--program_group_version -PG_VERSION	string	Value of the `VN` tag of the `PG` record to be created. If not supplied, the version is detected automatically.
--program_record_id -PG	string	The program record ID for the `PG` record(s) created by this tool. A suffix may be appended to this string to avoid collision with other program record IDs. Set to `null` to disable `PG` record creation. Default: 'MarkDuplicates'.
--read_name_regex	string	MarkDuplicates can use the tile and cluster positions to estimate the rate of optical duplication in addition to the dominant source of duplication, PCR, to provide a more accurate estimation of library size. By default (with no `--read_name_regex` specified), MarkDuplicates will attempt to extract coordinates using a split on `:`. Set `--read_name_regex` to `null` to disable optical duplicate detection. Note that without optical duplicate counts, library size estimation will be less accurate.
--read_one_barcode_tag	string	Read one barcode SAM tag (e.g. `BX` for 10x Genomics).
--read_two_barcode_tag	string	Read two barcode SAM tag (e.g. `BX` for 10x Genomics).
--reference_sequence -R	file	Reference sequence FASTA file. Only required when the input file is CRAM format.
--remove_duplicates	boolean_true	If set, do not write duplicates to the output file instead of writing them with the appropriate SAM flags set.
--remove_sequencing_duplicates	boolean_true	If set, remove 'optical' duplicates and other duplicates that appear to have arisen from the sequencing process instead of the library preparation process, even if `--remove_duplicates` is not set. If `--remove_duplicates` is set, all duplicates are removed and this option is ignored.
--sorting_collection_size_ratio	double	This number, plus the maximum RAM available to the JVM, determine the memory footprint used by some of the sorting collections. If you are running out of memory, try reducing this number. Default: 0.25.
--tag_duplicate_set_members	boolean_true	If set, for a read that appears in a duplicate set, add two tags. The first tag, `DS`, indicates the size of the duplicate set. The second tag, `DI`, represents a unique identifier for the duplicate set to which the record belongs.
--tagging_policy	string	Determines how duplicate types are recorded in the `DT` optional attribute. Default: 'DontTag'.
--validation_stringency	string	Validation stringency for all SAM files read by this program. Setting stringency to `SILENT` can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default: 'STRICT'.

Name

Type & Properties

--add_pg_tag_to_reads

boolean

--assume_sort_order

-ASO

string

--barcode_tag

string

--clear_dt

boolean

--comment

-CO

string

multiple

--create_index

boolean_true

--duplex_umi

boolean_true

--duplicate_scoring_strategy

-DS

string

--max_file_handles_for_read_ends_map

-MAX_FILE_HANDLES

integer

--max_optical_duplicate_set_size

long

--max_records_in_ram

integer

--molecular_identifier_tag

string

--optical_duplicate_pixel_distance

integer

--program_group_command_line

-PG_COMMAND

string

--program_group_name

-PG_NAME

string

--program_group_version

-PG_VERSION

string

--program_record_id

-PG

string

--read_name_regex

string

--read_one_barcode_tag

string

--read_two_barcode_tag

string

--reference_sequence

-R

file

--remove_duplicates

boolean_true

--remove_sequencing_duplicates

boolean_true

--sorting_collection_size_ratio

double

--tag_duplicate_set_members

boolean_true

--tagging_policy

string

--validation_stringency

string