This tool extracts reads from a BAM file based on alignment intervals. E.g if one is interested in a specific location this tool extracts the full reads from the location. The tool is also very usefull to create test data sets.


To get the help menu:

java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq -h
ExtractAlignedFastq - Select aligned FASTQ records

Usage: ExtractAlignedFastq [options]

  -l <value> | --log_level <value>
        Log level
  -h | --help
        Print usage
  -v | --version
        Print version
  -I <bam> | --input_file <bam>
        Input BAM file
  -r <interval> | --interval <interval>
        Interval strings
  -i <fastq> | --in1 <fastq>
        Input FASTQ file 1
  -j <fastq> | --in2 <fastq>
        Input FASTQ file 2 (default: none)
  -o <fastq> | --out1 <fastq>
        Output FASTQ file 1
  -p <fastq> | --out2 <fastq>
        Output FASTQ file 2 (default: none)
  -Q <value> | --min_mapq <value>
        Minimum MAPQ of reads in target region to remove (default: 0)
  -s <value> | --read_suffix_length <value>
        Length of common suffix from each read pair (default: 0)

This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals.

To run the tool:

java -jar Biopet-0.2.0.jar tool ExtractAlignedFastq \
--input_file myBam.bam --in1 myFastq_R1.fastq --out1 myOutFastq_R1.fastq --interval myTarget.bed
  • Note that this tool works for single end and paired end data. The above example can be easily extended for paired end data. The only thing one should add is: --in2 myFastq_R2.fastq --out2 myOutFastq_R2.fastq
  • The interval is just a genomic position or multiple genomic positions wherefrom one wants to extract the reads.


The output of this tool will be fastq files containing only mapped reads with the given alignment intervals extracted from the bam file.