Gaurav1983

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Gaurav1983
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  • Hi @bshifaw Thanks for your reply. I reduced the number of reads and now it finishes quickly for single reads but for paired reads it still took two days to finish. Would it be advantageous to pre filter the host reads to speed up the process? Wo…
  • Hi Sheila, The GVCFs were generated with HaplotypeCaller using below command. java -Djava.io.tmpdir=$temp -Xmx64g -jar $gatk/GenomeAnalysisTK.jar -T HaplotypeCaller -R $REF -I $output.bam -nct $Ncpu --emitRefConfidence GVCF --dbsnp $DBSNP -o $outp…
  • Hi, I am getting the above error with GenotypeGVCFs. Below is the Error stack trace. ERROR stack trace 2016/09/26 13:38:43: ERROR java.util.ConcurrentModificationException at java.util.LinkedList$ListItr.checkForComodification(LinkedList.…
  • Thanks for quick fix. I have include one more step of print read in my pipeline and It is working fine on test data.
  • folder uploaded in ftp server (BAQ_tag_error.tar.gz). Hope this will help.
  • Further to narrow down the problem, the intermediate bam file constructed (after alignment around indels) before running PrintReads is running fine with Unified Genotyper. I am using following command while running PrintReads: java -Xmx4g -Djava.io…
  • I am getting above error with latest version of GATK too
  • I was looking at a bug "Fixing BQSR/BAQ bug". Could this be the problem for above error. Further, Can you please elaborate on the fix? (https://github.com/broadgsa/gatk/commit/46b6d3214381e80ba7ee0f5df6432511a995216c)
  • I am using GenomeAnalysisTK-2.3-9-ge5ebf34 version.