What it does
Je MarkDupes: Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules taking into account molecular barcodes (Unique Molecular Identifiers or UMIs) found in read header. All records are then either written to the output file with the duplicate records flagged or trashed.
Input file is a bam file.
Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
Know what you are doing
You will want to read the documentation.
Parameter list
This is an exhaustive list of options:
INPUT=String
I=String
One or more input SAM or BAM files to analyze. Must be coordinate sorted.
Default value: null. This option may be specified 0 or more times.
OUTPUT=File
O=File
The output file to write marked records to
Required.
MISMATCHES=Integer
MM=Integer
Number of MisMatches (inclusive) to still consider two Unique Molecular Identifiers
(UMIs) the same i.e. this option buffers for sequencing errors.
Indeed, in case of a sequencing error, 2 duplicate reads would not be considered
duplicates anymore.
Note that N are not considered mismatches during comparison ie ATTNGG and NTTANG are seen
as the same barcode and these two reads would be flagged duplicates.
This option takes a single value even when several barcodes are present (see SLOTS).
Note that when declaring several barcodes (see SLOTS) AND providing a predefined set
of barcodes (see BC option), the MM value is applicable in each lookup. When a predefined
set of barcodes is NOT given, the different barcodes (SLOTS) are concatenated first and
the MM value is therefore considered *overall* as the concatenated code is seen as a
unique code.
MM=null is like MM=0
Use the minimum Hamming distance of the original barcode set (if applicable).
Required.
MAX_NUMBER_OF_N=Integer
MAX_N=Integer
Maximum number of Ns a molecular code can contain (inclusive). Above this value, reads
are placed in a UNDEF group.
More precisely, these 'too degenarate' codes will not :
* be compared to the list of predefined codes [predefined code list situation ie BC
option given] nor
* be considered as a potential independent code [no predefined code list situation ie
BC option not given]
Default value is the MISMATCHES number.
Note that when declaring several barcodes (see SLOTS) AND providing a predefined set
of barcodes (see BC option), the MAX_N value is applicable to each barcode. When a
predefined set
of barcodes is NOT given, the different barcodes (SLOTS) are concatenated first and the
MAX_N value
is therefore considered *overall*.
Default value: null.
SLOTS=Integer
SLOTS=Integer
Where to find the UMIs (and only the UMIs) in the read name once read name has been
tokenized using the SPLIT character (e.g. ':').
By default, the UMI is considered to be found at the end of the read header i.e. after
the last ':'. Use this option to indicate other or additional UMI positions (e.g.
multiple UMIs present in read header.
IMPORTANT: counting starts at 1 and negative numbers can be used to start counting from
the end.
For example, consider the following read name that lists 3 different barcodes in the end:
HISEQ:44:C6KC0ANXX:8:2112:20670:79594:CGATGTTT:GATCCTAG:AAGGTACG
to indicate that the three barcodes are molecular codes, use
SLOTS=-1 SLOTS=-2 SLOTS=-3
if only the 2 last ones should be considered (the third one being a sample encoding
barcode), use
SLOTS=-1 SLOTS=-2
Default value: null. This option may be specified 0 or more times.
BARCODE_FILE=File
BC=File
Pre-defined list of UMIs that can be expected. Format: one column text file, one barcode
per line. All UMIs MUST have the same length.
Default value: null.
TRIM_HEADERS=Boolean
T=Boolean
Should barcode information be removed from read names in the output BAM?
Default value: false. This option can be set to 'null' to clear the default value.
Possible values: {true, false}
TSLOTS=Integer
TSLOTS=Integer
Where to find *all* barcode(s) (i.e. sample encoding and UMIs) in the read name once has
been tokenized using the SPLIT character (e.g. ':').
This option is only considered when TRIM_HEADERS=true. When TSLOTS is ommited while
TRIM_HEADERS=true, the values of SLOTS apply.
IMPORTANT : counting starts at 1 and negative numbers can be used to start counting from
the end.
See SLOT help for examples.
Default value: null. This option may be specified 0 or more times.
SPLIT_CHAR=String
SPLIT=String
Character to use to split up the read header line, default is ':'.
Default value: ':'. This option can be set to 'null' to clear the default value.
INPUT=String
I=String
One or more input SAM or BAM files to analyze. Must be coordinate sorted.
Default value: null. This option may be specified 0 or more times.
OUTPUT=File
O=File
The output file to write marked records to Required.
METRICS_FILE=File
M=File
File to write duplication metrics to Required.
COMMENT=String
CO=String
Comment(s) to include in the output file's header.
Default value: null. This option may be specified 0 or more times.
REMOVE_DUPLICATES=Boolean
If true do not write duplicates to the output file instead of writing them with
appropriate flags set.
Default value: false. This option can be set to 'null' to clear
the default value.
Possible values: {true, false}
ASSUME_SORTED=Boolean
AS=Boolean
If true, assume that the input file is coordinate sorted even if the header says
otherwise.
Default value: false. This option can be set to 'null' to clear the default
value.
Possible values: {true, false}
DUPLICATE_SCORING_STRATEGY=ScoringStrategy
DS=ScoringStrategy
The scoring strategy for choosing the non-duplicate among candidates.
Default value: SUM_OF_BASE_QUALITIES. This option can be set to 'null' to clear the default value.
Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH}
READ_NAME_REGEX=String
Regular expression that can be used to parse read names in the incoming SAM file. Read
names are parsed to extract three variables: tile/region, x coordinate and y coordinate.
These values are used to estimate the rate of optical duplication in order to give a more
accurate estimated library size. Set this option to null to disable optical duplicate
detection. The regular expression should contain three capture groups for the three
variables, in order. It must match the entire read name. Note that if the default regex
is specified, a regex match is not actually done, but instead the read name is split on
colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be
tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements
are assumed to be tile, x and y values.
Default value:
[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. This option can be set to 'null' to
clear the default value.
OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer
The maximum offset between two duplicte clusters in order to consider them optical
duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
which case 50-100 is more normal.
Default value: 100. This option can be set to 'null'
to clear the default value.