Table 1

SAMQA Technical Tests

Technical Tests

Examples


Header Consistency

Consistency of chromosome identifiers, presence of read groups and sequence dictionary, valid reference sequence.


Specification Adherence

Correct regular expression for flag value, query name, mapping position, mate mapping position, inferred insert size, etc.


Functional Relationships

Incorrect flags set (e.g. Reads not mapped in a proper pair, with proper pair flag set), adjacent indel present in CIGAR value, invalid or missing tag NM, and functional dependent fields do not align or are invalid.


This list includes errors that are defined by the SAM format. Errors may be introduced at multiple levels as described in the "Examples" column. These tests are run in SAMQA using the Picard toolset from SAMtools.

Robinson et al. BMC Genomics 2011 12:419   doi:10.1186/1471-2164-12-419

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