Нетривиальная задача по конвертации FASTQ в BAM. Например, для того, чтобы отправить данные из какой-то коллекции в YFull.
http://www.y-str.org/2015/08/srafastq-to-bam-kit.htmlMost Ancient DNA are uploaded as SRA or FASTQ files. This kit is developed to allow anyone to download and convert SRA / FASTQ files to BAM files. Once converted, it can be further processed using BAM Analysis Kit, which can be further used for genetic genealogy.