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NOTE: This tool does not properly work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.
NOTE: This tool does not properly work on templates that have more than 2 segments. It does not properly match reads when more than 2 reads have the same read name.
NOTE: Dedup cannot read from stdin since it reads the input file twice.
Potential future features:
Potential future features:
Rules:
Rules:
* Skip Unmapped Reads, they are not marked as duplicate
* Skip Unmapped Reads, they are not marked as duplicate
* Reads whose mate is unmapped are treated as single-end
* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:
* Mark a Single-End Read Duplicate (or remove it if configured to do so) if:
*# A paired-end record has the same key (even if the pair is not proper/the mate is unmapped/the mate is not found)<br/>-OR-
*# A paired-end record has the same key (even if the pair is not proper/the mate is not found)<br/>-OR-
*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])
*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])
* Mark both Paired-End Reads Duplicate if:
* Mark both Paired-End Reads Duplicate if:
This code assumes that at most 1000 bases are clipped at the start of a read.
This code assumes that at most 1000 bases are clipped at the start of a read.
Deduping requires two passes through the file, so cannot read from stdin.
==Handling Recalibration==
==Handling Recalibration==
and exit when trying to run on an already mark-duplicated BAM
and exit when trying to run on an already mark-duplicated BAM
--excludeFlags <flag> : exclude reads with any of these flags set when determining or marking duplicates
--excludeFlags <flag> : exclude reads with any of these flags set when determining or marking duplicates
by default (0x304): exclude unmapped, secondary reads, and QC failures
by default (0xB04): exclude unmapped, secondary reads, QC failures, and supplementary reads
--verbose : Turn on verbose mode
--verbose : Turn on verbose mode
--noeof : Do not expect an EOF block on a bam file.
--noeof : Do not expect an EOF block on a bam file.
== Required Parameters ==
== Required Parameters ==
{{inBAMInputFile}}
{{inBAMInputFile|noStdin=1}}
Note: The input file must be sorted by coordinate.
Note: The input file must be sorted by coordinate.
=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===
=== Skip Records with any of the Specified Flags (<code>--excludeFlags</code>)===
Skip records with any of the specified flags set, default 0x304
Skip records with any of the specified flags set, default 0xB04
By default skips reads with any of the following flags set:
By default skips reads with any of the following flags set:
* secondary alignment
* secondary alignment
* fails QC checks
* fails QC checks
* supplementary reads
Secondary (0x100) and Supplementary (0x800) reads currently must be excluded.
=== Turn on Verbose Mode (<code>--verbose</code>) ===
=== Turn on Verbose Mode (<code>--verbose</code>) ===
