Create BFQ files from a BAM file for use by the maq aligner. BFQ is a binary version of the FASTQ file format. This tool creates bfq files from a BAM file for use by the maq aligner.
java -jar picard.jar BamToBfq I=input.bam ANALYSIS_DIR=analysis_dir OUTPUT_FILE_PREFIX=output_file_1 PAIRED_RUN=false
INPUT (File) The BAM file to parse. Required.
ANALYSIS_DIR (File) The analysis directory for the binary output file. Required.
FLOWCELL_BARCODE (String) Flowcell barcode (e.g. 30PYMAAXX). Required. Cannot be used in conjuction with option(s) OUTPUT_FILE_PREFIX
LANE (Integer) Lane number. Default value: null. Cannot be used in conjuction with option(s) OUTPUT_FILE_PREFIX
OUTPUT_FILE_PREFIX (String) Prefix for all output files Required. Cannot be used in conjuction with option(s) FLOWCELL_BARCODE (F) LANE (L)
READS_TO_ALIGN (Integer) Number of reads to align (null = all). Default value: null.
READ_CHUNK_SIZE (Integer) Number of reads to break into individual groups for alignment Default value: 2000000. This option can be set to 'null' to clear the default value.
PAIRED_RUN (Boolean) Whether this is a paired-end run. Required. Possible values: {true, false}
RUN_BARCODE (String) Deprecated option; use READ_NAME_PREFIX instead Default value: null. Cannot be used in conjuction with option(s) READ_NAME_PREFIX
READ_NAME_PREFIX (String) Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq) Default value: null.
INCLUDE_NON_PF_READS (Boolean) Whether to include non-PF reads Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
CLIP_ADAPTERS (Boolean) Whether to clip adapters from the reads Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
BASES_TO_WRITE (Integer) The number of bases from each read to write to the bfq file. If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written. Default value: null.