BAM Tools

Convert SAM/BAM to FastQ

Extract reads from SAM/BAM files and convert them to FastQ.

Select the corresponding input files, single and paired-end are possible.

This page allows configuring under what circumstances reads are considered “aligned”, i.e. they will be organized together with the aligned output fastq files.

  • Proper Pair Filter: Decide if both reads have to be aligned or if one is enough.

  • Read Directions: Choose in which direction the read pairs have to align.

  • Minimum MAPQ: Filter out low-quality alignments (0 - 255).

Select where to save aligned and unaligned reads respectively and if the output should be compressed individually as in .fastq.gz.