Keep only flow based reads that are well-formed

Category Read Filters

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Overview

Tests whether a flow based read is "well-formed" -- that is, is free of major internal inconsistencies and issues that could lead to errors downstream. If a read passes this filter, the rest of the engine should be able to process it without blowing up. Note that checks already present in WellformedReadFilter are not duplicated here.

Well-formed flow based reads definition

• Flow order: read group must have flow order
• Quality: should be symtrical within each hmer.
• tp attribute: should be symtrical within each hmer.
• tp attribute: tp+hmer_length should be within [0, maxhmer],
• Hardclipped hmer: is excempted from above checks.

Additional references

See these additional references.

• ValidAlignmentStartReadFilter
• ValidAlignmentEndReadFilter
• AlignmentAgreesWithHeaderReadFilter
• HasReadGroupReadFilter
• MatchingBasesAndQualsReadFilter
• ReadLengthEqualsCigarLengthReadFilter
• SeqIsStoredReadFilter
• CigarContainsNoNOperator
• ReadGroupHasFlowOrderReadFilter
• HmerQualitySymetricReadFilter
• FlowBasedTPAttributeValidReadFilter
• FlowBasedTPAttributeSymetricReadFilter

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GATK version 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.