Binary Alighnment/Map files (BAM) are the preferred SRA submission format. BAM is a compressed version of the Sequence Alignment/Map (SAM) format BAM files can be decompressed to a human-readable text format (SAM) using SAM/BAM-specific utilities and can contain unaligned sequences as well. BAM file creation. This page assumes you have the 3.0 SMRTanalysis stack installed. There is no other supported way to build BAM files according to our requirements. So, for example, if you do not have bax2bam available, there is no other supported way to build a compliant BAM file adhering to our requirements.
NOTE: this page is now available atSAMTools provides various tools for manipulating alignments in the SAM/BAM format. The SAM (Sequence Alignment/Map) format (BAM is just the binary form of SAM) is currently the de facto standard for storing large nucleotide sequence alignments. If you are dealing with high-throughput sequencing data, at some point you will probably have to deal with SAM/BAM files, so familiarise yourself with them!Here are some basic commands to get your started. For more information on the SAM/BAM format see. Samtools flagstat samtools flagstat NA06984.chrom20.ILLUMINA.bwa.CEU.lowcoverage.20111114.bam16874858 + 0 in total (QC-passed reads + QC-failed reads)290281 + 0 duplicates36683299 + 0 mapped (97.21%)46816083 + 0 paired in sequencing53408650 + 0 read163407433 + 0 read276348470 + 0 properly paired (93.14 No value assigned)86432965 + 0 with itself and mate mapped9191559 + 0 singletons (2.81No value assigned)1057057 + 0 with mate mapped to a different chr1145762 + 0 with mate mapped to a different chr (mapQ=5)To confirm some of the numbers returned by flagstat.
. Bob Handsaker. Alec Wysoker. Tim Fennell. Jue Ruan.
Nils Homer. Gabor Marth.Type of formatExtended fromWebsiteSequence Alignment Map (SAM) is a text-based originally for storing to a developed by and Bob Handsaker et al. It is widely used for storing data, such as sequences, generated by technologies, and the standard has been broadened to include unmapped sequences.
The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the and across the, the, and throughout the. Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. Sequencing reads) to (a) reference sequence(s). It may contain base-call and alignment qualities and other data.