Purpose

Reads a SAM/BAM dataset and report on its validity.

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/):

MODE=Mode
M=Mode                        Mode of output  Default value: VERBOSE. This option can be set to 'null' to clear the
                              default value. Possible values: {VERBOSE, SUMMARY}

IGNORE=Type                   List of validation error types to ignore.  Possible values: {INVALID_QUALITY_FORMAT,
                              INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
                              INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
                              INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
                              INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
                              INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
                              ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
                              INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
                              MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
                              MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
                              READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
                              MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
                              MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
                              MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
                              E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
                              POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
                              HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
                              INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
                              DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
                              DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
                              MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
                              specified 0 or more times.

MAX_OUTPUT=Integer
MO=Integer                    The maximum number of lines output in verbose mode  Default value: 100. This option can
                              be set to 'null' to clear the default value.

REFERENCE_SEQUENCE=File
R=File                        Reference sequence file, the NM tag check will be skipped if this is missing  Default
                              value: null.

IGNORE_WARNINGS=Boolean       If true, only report errors and ignore warnings.  Default value: false. This option can
                              be set to 'null' to clear the default value. Possible values: {true, false}

VALIDATE_INDEX=Boolean        If true and input is a BAM file with an index file, also validates the index.  Default
                              value: true. This option can be set to 'null' to clear the default value. Possible
                              values: {true, false}

IS_BISULFITE_SEQUENCED=Boolean
BISULFITE=Boolean             Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
                              counted as an error in computing the value of the NM tag.  Default value: false. This
                              option can be set to 'null' to clear the default value. Possible values: {true, false}

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .