Quentin Chartreux

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Recent activity by Quentin Chartreux Sort by recent activity Recent activity Votes
  • Dragen-gatk pipeline reference


    Some things are not very clear to me regarding the references used. According to your article de should use dragmap with a hash table generated using an alt-mask-bed. However in the read me present...

  • MergeBamAlignement error


    Dear gatk team, I use dragmap to align with a unmapped bam as input and i produce a bam.  Then i try to use MergeBamAlignement but i get this error:  "Aligned record iterator (A00957:55:HGJHFDSXY:4...

  • Haplotype caller error file not found


    Dear gatk team, When I use haplotypecaller I have a problem that the same script will sometimes work correctly and provide the gvcf and sometimes not. This happens for the same file, ie I can run t...

  • GenotypeGVCFs error IndexOutOfBoundsException


    I try to perform joint genotyping with genotypeGVCF.  Before i run haplotypecaller then Genomicsdbiimport and now genotypesGVCF.  I used gatk  I run Genomicsdbiimport by interval so i woul...

  • MarkduplicateSpark error


    a) GATK version used: Exact command used: gatk \--java-options "-Xmx${SLURM_MEM_PER_NODE}M" \MarkDuplicatesSpark \-I ${BAM_INPUT_DIR}/${BAM_INPUT} \-O ${BAM_OUTPUT_DIR}/${BAM_OUTPUT} \-M ...

  • VQSR different tuto ?


    Hello all,  I'm working with WGS from germline (for rare disease) but for VQSR step i'm a bit lost because the command (option) are not the same between the tool page and the tuto at these page.  I...

  • GenotypeGVCFs is too long


    I try to use GenotypeGVCFs for human WGS data.  I use GATK with the following command :  gatk --java-options "-Xmx20g -Xms20g" GenotypeGVCFs \-R ${REF_Genome} \-V gendb://${VCF_database_DIR...

  • Haplotypecaller too long ?


    Dear GATK team,  I would like to do variant calling with haplotypecaller in gvcf mode for human genome 30X (aligned to hg38) I use GATK, I do the variant calling by interval with for each i...

  • HaplotypeCallerSpark


    Hi,  I try to use gatk haplotypecallerspark. I have gatk My data are human WGS (40X). Each bam is arround 100 Go. I try this command, but it stops less than 2 minutes after begining (i don...

  • BQSR Pipeline Spark

    I want to use BQSR Pipeline Spark from gatk on human WGS.  I ran the command first on a single bam file, it took about 3 hours so it's ok. On the other hand after I launched exactly the sam...