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issues with FindCoveredIntervals

Hi,
I'm using FindCoveredIntervals with GATK 3.8 and running the following:

java -jar GenomeAnalysisTK.jar -T FindCoveredIntervals -R reference.fasta -I input.bam -cov 10 -minBQ 30 -minMQ 30 --uncovered -o output.list

When I look at the BAM file with DepthOfCoverage I see that there are many intervals with coverage below 10 that are not recognized as uncovered intervals. What can be the reason for that? Is this related to the base quality threshold, i.e. if these positions are covered with less than 10 read bases but all with BQ > 30, does it consider them as covered?

Best,
Nicola

Answers

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited February 26

    Hi @NicRamb

    if these positions are covered with less than 10 read bases but all with BQ > 30, does it consider them as covered

    It should consider them as uncovered in the output as it uses an 'and' operator with multiple options. Please try the latest version of GATK4.1. Most bug are fixed in the latest release. If the problem persists I can have one of the dev team members look into it.

  • NicRambNicRamb Member
    Hi @bhanuGandham

    Thanks for your reply. I tried with both GATK 4.1 and GATK 4.0, but I cannot find the FindCoveredIntervals tool in the Tool Documentation Index. Has it been removed from latest releases? If so, are there any other tools in the 4.1 version that have the same function or is there the possibility to solve the problem in the 3.8 one?
  • manolismanolis Member ✭✭
    edited February 27

    Hi @bhanuGandham just a question about FindCoveredIntervals. The '--activeRegionIn' option in gatk3.8.1 is like the '-L' option in gatk4 or is there a similar option to '-L' in gatk3? I'm interstring too about similar tools in gatk4, to filter by coverage... Thanks

    Post edited by manolis on
  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hello @NicRamb and @manolis - I asked the developer and there is not a comparable tool to FindCoveredIntervals
    Number of bases to cache when querying feature tracks. in the latest release.

  • manolismanolis Member ✭✭
  • NicRambNicRamb Member
    ok, thank you, @AdelaideR
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