---
title: "BAM Tools"
canonical: "https://help.biobam.com/space/OBD/2464972830/BAM%20Tools"
format: markdown
---
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.