Alignment Output
After sorting the reads, Isaac Alignment generates compressed binary alignment output files, called BAM (*.bam) files, using the following process:
| • | Marking duplicates—Detection of duplicates is based on the location and observed length of each fragment. Isaac Alignment identifies and marks duplicates even when they appear on oversized fragments or chimeric fragments. |
| • | Realigning indels—Isaac Alignment tracks previously detected indels over a window large enough for the current read length. Isaac Alignment then applies the known indels to all reads with mismatches. |
| • | Generating BAM files—The first step in BAM file generation is creation of the BAM record. This record contains all required information, except the name of the read. Isaac Alignment reads data from the FASTQ header for each read to generate the read names. Data are then compressed into blocks of 64 kb or less to create the BAM file. |