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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Problem making UG work with ReducedReads

sasgarisasgari Member
edited September 2012 in Ask the GATK team

Hi,

I'm trying to use GATK release2.0 with my nine exome-seq samples, following the steps on best practice I generated per-sample, ready-to-process .bam files and then used -T ReduceReads to generate .reduced.bam files for the next step (-T UnifiedGenotyper). When using these .reduced.bam files as UG input I receive this error message: "##### ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?" if I take my original .bam files as input things work smoothly. Do you have any idea what causes the problem?

Thanks a lot,
Samira

Here is the command lines I use:

java -Xmx4g -jar $GATKv4 \
    -R $GATK_BUNDLE/ucsc.hg19.fasta \
    -T ReduceReads \
    -L $capture_library.bed \
    -I $i.recal_s.bam \
    -o $i.reduced.bam

 java -jar $GATKv4 \
    -T HaplotypeCaller \
    -R $GATK_BUNDLE/ucsc.hg19.fasta \
    -I InputReducedBams.list \
    -L $capture_library.bed \
    --dbsnp GATK_BUNDLE/dbsnp_135.hg19.vcf \
    -o raw.snp.indel.UnifiedGenotyper.rsv.vcf
Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Hi there,

    When you say version 2.0, do you mean literally 2.0, or a later version, 2.x? Some bugs have been fixed since 2.0 itself, so if you're not using the latest version I encourage you to try it. Currently we're on 2.1-8.

    If that's still not working we'll take a look at your problem.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Accepted Answer

    Hi there,

    When you say version 2.0, do you mean literally 2.0, or a later version, 2.x? Some bugs have been fixed since 2.0 itself, so if you're not using the latest version I encourage you to try it. Currently we're on 2.1-8.

    If that's still not working we'll take a look at your problem.

  • Thanks a lot! Problem solved with upgrading to the latest version, btw, for future readers: in my original msg, 2nd part, I meant to write -T Unifiedgenotyper and not -T HaplotypeCaller.

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