MergeBamAlignment v4.1.8.0
Version of tools in docker image
Tool
Version
Location
gatk
4.1.8.0
broadinstitute/gatk:4.1.8.0
CWL
CWL specification 1.0
Use example_inputs.yaml to see the inputs to the cwl
Example Command using toil:
> toil-cwl-runner gatk_merge_bam_alignment_4.1.8.0.cwl example_inputs.yamlUsage
usage: gatk_merge_bam_alignment_4.1.8.0.cwl [-h]
[--memory_per_job MEMORY_PER_JOB]
[--memory_overhead MEMORY_OVERHEAD]
[--number_of_threads NUMBER_OF_THREADS]
--unmapped_bam UNMAPPED_BAM
--reference REFERENCE
[--output_file_name OUTPUT_FILE_NAME]
[--add_mate_cigar]
[--add_pg_tag_to_reads]
[--aligned_bam ALIGNED_BAM]
[--aligned_reads_only]
[--aligner_proper_pair_flags]
[--attributes_to_remove ATTRIBUTES_TO_REMOVE]
[--attributes_to_retain ATTRIBUTES_TO_RETAIN]
[--attributes_to_reverse ATTRIBUTES_TO_REVERSE]
[--attributes_to_reverse_complement ATTRIBUTES_TO_REVERSE_COMPLEMENT]
[--clip_adapters]
[--clip_overlapping_reads]
[--expected_orientations EXPECTED_ORIENTATIONS]
[--hard_clip_overlapping_reads]
[--include_secondary_alignments]
[--is_bisulfite_sequence]
[--jump_size JUMP_SIZE]
[--matching_dictionary_tags MATCHING_DICTIONARY_TAGS]
[--max_insertions_or_deletions MAX_INSERTIONS_OR_DELETIONS]
[--min_unclipped_bases MIN_UNCLIPPED_BASES]
[--paired_run]
[--primary_alignment_strategy PRIMARY_ALIGNMENT_STRATEGY]
[--read1_aligned_bam READ1_ALIGNED_BAM]
[--read1_trim READ1_TRIM]
[--read2_aligned_bam READ2_ALIGNED_BAM]
[--read2_trim READ2_TRIM]
[--sort_order SORT_ORDER]
[--unmap_contaminant_reads]
[--unmapped_read_strategy UNMAPPED_READ_STRATEGY]
[--validation_stringency VALIDATION_STRINGENCY]
[--create_index]
[--create_md5_file]
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--memory_per_job MEMORY_PER_JOB
Memory per job in megabytes
--memory_overhead MEMORY_OVERHEAD
Memory overhead per job in megabytes
--number_of_threads NUMBER_OF_THREADS
--unmapped_bam UNMAPPED_BAM
Original SAM or BAM file of unmapped reads, which must
be in queryname order. Reads MUST be unmapped.
Required.
--reference REFERENCE
Reference sequence file. Required.
--output_file_name OUTPUT_FILE_NAME
Merged SAM or BAM file to write to. Required.
--add_mate_cigar Adds the mate CIGAR tag (MC) if true, does not if
false. Default value: true. Possible values: {true,
false}
--add_pg_tag_to_reads
Add PG tag to each read in a SAM or BAM Default value:
true. Possible values: {true, false}
--aligned_bam ALIGNED_BAM
SAM or BAM file(s) with alignment data. This argument
may be specified 0 or more times. Default value: null.
Cannot be used in conjunction with argument(s)
READ1_ALIGNED_BAM (R1_ALIGNED) READ2_ALIGNED_BAM
(R2_ALIGNED)
--aligned_reads_only Whether to output only aligned reads. Default value:
false. Possible values: {true, false}
--aligner_proper_pair_flags
Use the aligners idea of what a proper pair is rather
than computing in this program. Default value: false.
Possible values: {true, false}
--attributes_to_remove ATTRIBUTES_TO_REMOVE
Attributes from the alignment record that should be
removed when merging. This overrides
ATTRIBUTES_TO_RETAIN if they share common tags. This
argument may be specified 0 or more times. Default
value: null.
--attributes_to_retain ATTRIBUTES_TO_RETAIN
Reserved alignment attributes (tags starting with X,
Y, or Z) that should be brought over from the
alignment data when merging. This argument may be
specified 0 or more times. Default value: null.
--attributes_to_reverse ATTRIBUTES_TO_REVERSE
Attributes on negative strand reads that need to be
reversed. This argument may be specified 0 or more
times. Default value: [OQ, U2].
--attributes_to_reverse_complement ATTRIBUTES_TO_REVERSE_COMPLEMENT
Attributes on negative strand reads that need to be
reverse complemented. This argument may be specified 0
or more times. Default value: [E2, SQ].
--clip_adapters Whether to clip adapters where identified. Default
value: true. Possible values: {true, false}
--clip_overlapping_reads
For paired reads, clip the 3' end of each read if
necessary so that it does not extend past the 5' end
of its mate. Clipping will be either soft or hard
clipping, depending on CLIP_OVERLAPPING_READS_OPERATOR
setting. Hard clipped bases and their qualities will
be stored in the XB and XQ tags respectively. Default
value: true. Possible values: {true, false}
--expected_orientations EXPECTED_ORIENTATIONS
The expected orientation of proper read pairs.
Replaces JUMP_SIZE This argument may be specified 0 or
more times. Default value: null. Possible values: {FR,
RF, TANDEM} Cannot be used in conjunction with
argument(s) JUMP_SIZE (JUMP)
--hard_clip_overlapping_reads
If true, hard clipping will be applied to overlapping
reads. By default, soft clipping is used. Default
value: false. Possible values: {true, false}
--include_secondary_alignments
If false, do not write secondary alignments to output.
Default value: true. Possible values: {true, false}
--is_bisulfite_sequence
Whether the lane is bisulfite sequence (used when
calculating the NM tag). Default value: false.
Possible values: {true, false}
--jump_size JUMP_SIZE
The expected jump size (required if this is a jumping
library). Deprecated. Use EXPECTED_ORIENTATIONS
instead Default value: null. Cannot be used in
conjunction with argument(s) EXPECTED_ORIENTATIONS
(ORIENTATIONS)
--matching_dictionary_tags MATCHING_DICTIONARY_TAGS
List of Sequence Records tags that must be equal (if
present) in the reference dictionary and in the
aligned file. Mismatching tags will cause an error if
in this list, and a warning otherwise. This argument
may be specified 0 or more times. Default value: [M5,
LN].
--max_insertions_or_deletions MAX_INSERTIONS_OR_DELETIONS
The maximum number of insertions or deletions
permitted for an alignment to be included. Alignments
with more than this many insertions or deletions will
be ignored. Set to -1 to allow any number of
insertions or deletions. Default value: 1.
--min_unclipped_bases MIN_UNCLIPPED_BASES
If UNMAP_CONTAMINANT_READS is set, require this many
unclipped bases or else the read will be marked as
contaminant. Default value: 32.
--paired_run DEPRECATED. This argument is ignored and will be
removed. Default value: true. Possible values: {true,
false}
--primary_alignment_strategy PRIMARY_ALIGNMENT_STRATEGY
Strategy for selecting primary alignment when the
aligner has provided more than one alignment for a
pair or fragment, and none are marked as primary, more
than one is marked as primary, or the primary
alignment is filtered out for some reason. For all
strategies, ties are resolved arbitrarily. Default
value: BestMapq. BestMapq (Expects that multiple
alignments will be correlated with HI tag, and prefers
the pair of alignments with the largest MAPQ, in the
absence of a primary selected by the aligner.)
EarliestFragment (Prefers the alignment which maps the
earliest base in the read. Note that EarliestFragment
may not be used for paired reads.) BestEndMapq
(Appropriate for cases in which the aligner is not
pair-aware, and does not output the HI tag. It simply
picks the alignment for each end with the highest
MAPQ, and makes those alignments primary, regardless
of whether the two alignments make sense together.)
MostDistant (Appropriate for a non-pair-aware aligner.
Picks the alignment pair with the largest insert size.
If all alignments would be chimeric, it picks the
alignments for each end with the best MAPQ.)
--read1_aligned_bam READ1_ALIGNED_BAM
SAM or BAM file(s) with alignment data from the first
read of a pair. This argument may be specified 0 or
more times. Default value: null. Cannot be used in
conjunction with argument(s) ALIGNED_BAM (ALIGNED)
--read1_trim READ1_TRIM
The number of bases trimmed from the beginning of read
1 prior to alignment Default value: 0.
--read2_aligned_bam READ2_ALIGNED_BAM
SAM or BAM file(s) with alignment data from the second
read of a pair. This argument may be specified 0 or
more times. Default value: null. Cannot be used in
conjunction with argument(s) ALIGNED_BAM (ALIGNED)
--read2_trim READ2_TRIM
The number of bases trimmed from the beginning of read
2 prior to alignment Default value: 0.
--sort_order SORT_ORDER
The order in which the merged reads should be output.
Default value: coordinate. Possible values: {unsorted,
queryname, coordinate, duplicate, unknown}
--unmap_contaminant_reads
Detect reads originating from foreign organisms (e.g.
bacterial DNA in a non-bacterial sample),and unmap +
label those reads accordingly. Default value: false.
Possible values: {true, false}
--unmapped_read_strategy UNMAPPED_READ_STRATEGY
How to deal with alignment information in reads that
are being unmapped (e.g. due to cross-species
contamination.) Currently ignored unless
UNMAP_CONTAMINANT_READS = true. Note that the
DO_NOT_CHANGE strategy will actually reset the cigar
and set the mapping quality on unmapped reads since
otherwisethe result will be an invalid record. To
force no change use the DO_NOT_CHANGE_INVALID
strategy. Default value: DO_NOT_CHANGE. Possible
values: {COPY_TO_TAG, DO_NOT_CHANGE,
DO_NOT_CHANGE_INVALID, MOVE_TO_TAG}
--validation_stringency VALIDATION_STRINGENCY
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 value: STRICT.
This option can be set to 'null' to clear the default
value. Possible values: {STRICT,LENIENT, SILENT}
--create_index Whether to create a BAM index when writing a
coordinate-sorted BAM file. Default value: false.
Possible values: {true, false}
--create_md5_file Whether to create an MD5 digest for any BAM or FASTQ
files created. Default value: false. Possible values:
{true, false}Last updated