java -jar picard.jar ValidateSamFile I=input.bam MODE=SUMMARY
INPUT (File) Input SAM/BAM file Required.
OUTPUT (File) Output file or standard out if missing Default value: null.
MODE (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. Default value: null. 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) The maximum number of lines output in verbose mode Default value: 100. This option can be set to 'null' to clear the default value.
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) DEPRECATED. Use INDEX_VALIDATION_STRINGENCY instead. If true and input is a BAM file with an index file, also validates the index. Until this parameter is retired VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
INDEX_VALIDATION_STRINGENCY (IndexValidationStringency) If set to anything other than IndexValidationStringency.NONE and input is a BAM file with an index file, also validates the index at the specified stringency. Until VALIDATE_INDEX is retired, VALIDATE INDEX and INDEX_VALIDATION_STRINGENCY must agree on whether to validate the index. Default value: EXHAUSTIVE. This option can be set to 'null' to clear the default value. Possible values: {EXHAUSTIVE, LESS_EXHAUSTIVE, NONE}
IS_BISULFITE_SEQUENCED (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}
MAX_OPEN_TEMP_FILES (Integer) Relevant for a coordinate-sorted file containing read pairs only. Maximum number of file handles to keep open when spilling mate info to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the 'ulimit -n' command on a Unix system. Default value: 8000. This option can be set to 'null' to clear the default value.