Purpose
Merges alignment data from a SAM or BAM dataset with additional data stored in an unmapped BAM dataset and produces a third SAM or BAM dataset of aligned and unaligned reads.
Dataset collections - processing large numbers of datasets at once
This will be added shortly
Inputs, outputs, and parameters
Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.
From Picard documentation( http://broadinstitute.github.io/picard/):
UNMAPPED_BAM=File
UNMAPPED=File Original SAM or BAM file of unmapped reads, which must be in queryname order. Required.
ALIGNED_BAM=File
ALIGNED=File SAM or BAM file(s) with alignment data. This option may be specified 0 or more times.
Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED)
READ2_ALIGNED_BAM (R2_ALIGNED)
READ1_ALIGNED_BAM=File
R1_ALIGNED=File SAM or BAM file(s) with alignment data from the first read of a pair. This option may be
specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM
(ALIGNED)
READ2_ALIGNED_BAM=File
R2_ALIGNED=File SAM or BAM file(s) with alignment data from the second read of a pair. This option may
be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM
(ALIGNED)
PAIRED_RUN=Boolean
PE=Boolean This argument is ignored and will be removed. Required. Possible values: {true, false}
JUMP_SIZE=Integer
JUMP=Integer The expected jump size (required if this is a jumping library). Deprecated. Use
EXPECTED_ORIENTATIONS instead Default value: null. Cannot be used in conjuction with
option(s) EXPECTED_ORIENTATIONS (ORIENTATIONS)
CLIP_ADAPTERS=Boolean Whether to clip adapters where identified. Default value: true. Possible values: {true, false}
IS_BISULFITE_SEQUENCE=Boolean Whether the lane is bisulfite sequence (used when caculating the NM tag). Default value:
false. Possible values: {true, false}
ALIGNED_READS_ONLY=Boolean Whether to output only aligned reads. Default value: false. Possible values: {true, false}
MAX_INSERTIONS_OR_DELETIONS=Integer
MAX_GAPS=Integer 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.
ATTRIBUTES_TO_RETAIN=String Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over
from the alignment data when merging. This option may be specified 0 or more times.
ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides
ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more
times.
READ1_TRIM=Integer
R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default
value: 0.
READ2_TRIM=Integer
R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default
value: 0.
EXPECTED_ORIENTATIONS=PairOrientation
ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR,
RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction
with option(s) JUMP_SIZE (JUMP)
ALIGNER_PROPER_PAIR_FLAGS=Boolean
Use the aligner's idea of what a proper pair is rather than computing in this program.
Default value: false. Possible values: {true, false}
SORT_ORDER=SortOrder
SO=SortOrder The order in which the merged reads should be output. Default value: coordinate.
Possible values: {unsorted, queryname, coordinate}
PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy
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. 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 is 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 is also
for a non-pair-aware aligner, and 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. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq.
Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant}
CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not
extend past the 5' end of its mate. Default value: true. Possible values: {true, false}
INCLUDE_SECONDARY_ALIGNMENTS=Boolean
If false, do not write secondary alignments to output. Default value: true.
Possible values: {true, false}
ADD_MATE_CIGAR=Boolean
MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false}
Additional information
Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .