Avatar

Quentin Chartreux

Follow
  • Total activity 57
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 16

Posts

Recent activity by Quentin Chartreux Sort by recent activity Recent activity Votes

  • Dragen-gatk pipeline reference

    Answered
    1. Community
    2. General Discussion

    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...

    • Quentin Chartreux
    • 4 followers
    • 12 comments
    • 0 votes

  • MergeBamAlignement error

    Answered
    1. Community
    2. General Discussion

    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...

    • Quentin Chartreux
    • 3 followers
    • 5 comments
    • 0 votes

  • Haplotype caller error file not found

    Answered
    1. Community
    2. Germline

    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...

    • Quentin Chartreux
    • 2 followers
    • 6 comments
    • 0 votes

  • GenotypeGVCFs error IndexOutOfBoundsException

    Answered
    1. Community
    2. General Discussion

    I try to perform joint genotyping with genotypeGVCF.  Before i run haplotypecaller then Genomicsdbiimport and now genotypesGVCF.  I used gatk 4.2.2.0.  I run Genomicsdbiimport by interval so i woul...

    • Quentin Chartreux
    • 4 followers
    • 14 comments
    • 0 votes

  • MarkduplicateSpark error

    Answered
    1. Community
    2. General Discussion

    a) GATK version used: 4.2.0.0b) 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 ...

    • Quentin Chartreux
    • 2 followers
    • 1 comment
    • 0 votes

  • VQSR different tuto ?

    Answered
    1. Community
    2. General Discussion

    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...

    • Quentin Chartreux
    • 2 followers
    • 2 comments
    • 0 votes

  • GenotypeGVCFs is too long

    Answered
    1. Community
    2. Germline

    I try to use GenotypeGVCFs for human WGS data.  I use GATK 4.2.0.0 with the following command :  gatk --java-options "-Xmx20g -Xms20g" GenotypeGVCFs \-R ${REF_Genome} \-V gendb://${VCF_database_DIR...

    • Quentin Chartreux
    • 2 followers
    • 3 comments
    • 0 votes

  • Haplotypecaller too long ?

    Answered
    1. Community
    2. Germline

    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 4.2.0.0, I do the variant calling by interval with for each i...

    • Quentin Chartreux
    • 3 followers
    • 6 comments
    • 0 votes

  • HaplotypeCallerSpark

    Answered
    1. Community
    2. Germline

    Hi,  I try to use gatk haplotypecallerspark. I have gatk 4.2.0.0. 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...

    • Quentin Chartreux
    • 2 followers
    • 1 comment
    • 0 votes

  • BQSR Pipeline Spark

    1. Community
    2. Germline

    I want to use BQSR Pipeline Spark from gatk 4.2.0.0 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...

    • Quentin Chartreux
    • 2 followers
    • 3 comments
    • 0 votes