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File format are sets of defined rules to organise a specific type of data. Common file format in bioinformatics include FASTA, FASTQ, SAM, BAM, VCF.

10
votes
2answers
The SAM specification indicates that each read group must have a unique ID field, but does not mark any other field as required. I have also discovered that htsjdk throws exceptions if the sample (S …
asked Jun 9 '17 by mattm
6
votes
1answer
I am trying to understand how the MD:Z tag is used. The following is from the SAM Optional Fields Specification, which gives an example but is not thorough. The MD field aims to achieve SNP/indel …
asked Jun 13 '17 by mattm
5
votes
1answer
From SAM Optional Fields Specification the NM field is Edit distance to the reference, including ambiguous bases but excluding clipping Assuming both the MD and CIGAR are present, is the edit d …
asked Jun 13 '17 by mattm