Converts a FASTQ file to an unaligned BAM or SAM file. This tool extracts read sequences and base qualities from the input FASTQ file and writes them out to a new file in unaligned BAM (uBAM) format. Read group information can be provided on the command line. Three versions of FASTQ quality scales are supported: FastqSanger, FastqSolexa and FastqIllumina (see http://maq.sourceforge.net/fastq.shtml for details). Input FASTQ files can be in GZip format (with .gz extension).
java -jar picard.jar FastqToSam F1=file_1.fastq O=fastq_to_bam.bam SM=for_tool_testing
FASTQ (File) Input fastq file (optionally gzipped) for single end data, or first read in paired end data. Required.
FASTQ2 (File) Input fastq file (optionally gzipped) for the second read of paired end data. Default value: null.
USE_SEQUENTIAL_FASTQS (Boolean) Use sequential fastq files with the suffix _###.fastq or _###.fastq.gz Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
QUALITY_FORMAT (FastqQualityFormat) A value describing how the quality values are encoded in the input FASTQ file. Either Solexa (phred scaling + 66), Illumina (phred scaling + 64) or Standard (phred scaling + 33). If this value is not specified, the quality format will be detected automatically. Default value: null. Possible values: {Solexa, Illumina, Standard}
OUTPUT (File) Output SAM/BAM file. Required.
READ_GROUP_NAME (String) Read group name Default value: A. This option can be set to 'null' to clear the default value.
SAMPLE_NAME (String) Sample name to insert into the read group header Required.
LIBRARY_NAME (String) The library name to place into the LB attribute in the read group header Default value: null.
PLATFORM_UNIT (String) The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
PLATFORM (String) The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
SEQUENCING_CENTER (String) The sequencing center from which the data originated Default value: null.
PREDICTED_INSERT_SIZE (Integer) Predicted median insert size, to insert into the read group header Default value: null.
PROGRAM_GROUP (String) Program group to insert into the read group header. Default value: null.
PLATFORM_MODEL (String) Platform model to insert into the group header (free-form text providing further details of the platform/technology used) Default value: null.
COMMENT (String) Comment(s) to include in the merged output file's header. Default value: null. This option may be specified 0 or more times.
DESCRIPTION (String) Inserted into the read group header Default value: null.
RUN_DATE (Iso8601Date) Date the run was produced, to insert into the read group header Default value: null.
SORT_ORDER (SortOrder) The sort order for the output sam/bam file. Default value: queryname. This option can be set to 'null' to clear the default value. Possible values: {unsorted, queryname, coordinate, duplicate}
MIN_Q (Integer) Minimum quality allowed in the input fastq. An exception will be thrown if a quality is less than this value. Default value: 0. This option can be set to 'null' to clear the default value.
MAX_Q (Integer) Maximum quality allowed in the input fastq. An exception will be thrown if a quality is greater than this value. Default value: 93. This option can be set to 'null' to clear the default value.
STRIP_UNPAIRED_MATE_NUMBER (Boolean) Deprecated (No longer used). If true and this is an unpaired fastq any occurrence of '/1' or '/2' will be removed from the end of a read name. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
ALLOW_AND_IGNORE_EMPTY_LINES (Boolean) Allow (and ignore) empty lines Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}