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Quentin Chartreux

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Latest activity by Quentin Chartreux
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    Quentin Chartreux commented,

    Genevieve Brandt (she/her)  I used gatk 4.2.3.0 with the following command: gatk --java-options "-Xmx${MEMORYxmx}M" ValidateSamFile \-I ${BAM_DIR}/${BAM} \-M SUMMARY \-O ${BAM_DIR}/${BAM/.bam/.txt}...

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    Quentin Chartreux commented,

    Thank you for your reply. I had indeed seen this post, I tried to sort the bam with samtools sort -n (the ubam and the bam aligned) but even in this case mergebamalignment gives this error. But the...

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    Quentin Chartreux created a post,

    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...

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    Quentin Chartreux commented,

    Hi Genevieve Brandt (she/her) I just tried. It seems to be working. I just had an error on 2 interval of type out of memory so I will try to increase the memory (currently I do it in parallel on 50...

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    Quentin Chartreux commented,

    Other question : The dragen mode of haplotypecaller can (should ?) Be use for variant calling on rna seq data ?

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    Quentin Chartreux commented,

    I try this New pipeline and it's really good. But two point : First, dragmap is very long (16h vs 7h for bwa mem2 for the same sample ans ressources). Second, it's not clear for me if after singl...

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    Quentin Chartreux commented,

    Hi Genevieve Brandt (she/her)   I asked the administrators of our cluster, we can not find out where the problem comes from, especially since the file in question is indeed created by haplotypecall...

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    Quentin Chartreux commented,

    It's not an important error as at the end it work, but it's a bit annoying to have the job running for 2 hours to ultimately fail without really knowing why and only being able to restart it, hopin...

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    Quentin Chartreux commented,

    Hi Genevieve Brandt (she/her) In the log it's written :   -I /shared/projects/gentaumix/processed_data_set5/03_Alignment/D_recal/G632_DA_C002A5Q_1_H5N3JDSX2.DUAL2.trimmed.align.filtered.dedup.fixed...

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    Quentin Chartreux created a post,

    Haplotype caller error file not found

    Answered

    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...