Verify mate-pair information between mates and fix if needed.This tool ensures that all mate-pair information is in sync between each read and its mate pair. If no OUTPUT file is supplied then the output is written to a temporary file and then copied over the INPUT file. Reads marked with the secondary alignment flag are written to the output file unchanged.
java -jar picard.jar FixMateInformation I=input.bam O=fixed_mate.bam
INPUT (File) The input file to check and fix. Default value: null. This option may be specified 0 or more times.
OUTPUT (File) The output file to write to. If no output file is supplied, the input file is overwritten. Default value: null.
SORT_ORDER (SortOrder) Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate}
ASSUME_SORTED (Boolean) If true, assume that the input file is queryname 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}
ADD_MATE_CIGAR (Boolean) Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
IGNORE_MISSING_MATES (Boolean) If true, ignore missing mates, otherwise will throw an exception when missing mates are found. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}