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WebFASTQ to BAM / CRAM. Sequencing instruments produce unaligned data, typically in FASTQ format. It is possible to store unaligned data in BAM or CRAM, and indeed it may be preferable as it permits meta-data in the header and per-record auxiliary tags, however in this workflow we consider the end product to be a sorted aligned BAM or CRAM file so … Web1. Generate an unmapped BAM from FASTQ, aligned BAM or BCL. If you have raw reads data in BAM format with appropriately assigned read group fields, then you can start with … hammacher ortho