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Problem making UG work with ReducedReads

Posts: 6Member
edited September 2012

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 \
-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
Tagged:

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.

Geraldine Van der Auwera, PhD

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.

Geraldine Van der Auwera, PhD

• Posts: 6Member

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.