SAMQA: error classification and validation of high-throughput sequenced read data

BMC Genomics

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.

ISSN: 1471-2164