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Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Picards NEAR_AMPLICON_BASES

mberrymberry Cape TownMember

Hi
The description of NEAR_AMPLICON_BASES in Picard is defined as "The number of PF aligned bases that mapped to within a fixed interval of an amplified region, but not on a baited region."
What is this fixed interval and is there a way to change how many bases it covers?

Thanks

Tagged:

Issue · Github
by Sheila

Issue Number
1094
State
closed
Last Updated
Assignee
Array
Milestone
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Closed By
dekling

Best Answer

Answers

  • deklingdekling Broad InstituteMember

    Hello @mberry:
    I believe that you are referring to sequences that are within the specified target regions that were were either missed or not included when designing the bait regions. For example, a bait region might be specific to an exon, but the target region might include sequence extending beyond an intron/exon boundary. Thus, you might have amplified regions that are not part of the baited region but are within the target region, which is what this metric is telling us.

    I believe the number of bases covered can be changed by adjusting the size of the target regions within the input interval file. Let us know if you have more questions.

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