
Quentin Chartreux
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Recent activity by Quentin Chartreux Sort by recent activity-
Dragen-gatk pipeline reference
AnsweredSome 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...
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MergeBamAlignement error
AnsweredDear 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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Haplotype caller error file not found
AnsweredDear 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...
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GenotypeGVCFs error IndexOutOfBoundsException
AnsweredI 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...
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MarkduplicateSpark error
Answereda) 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 ...
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VQSR different tuto ?
AnsweredHello 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...
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GenotypeGVCFs is too long
AnsweredI 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...
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Haplotypecaller too long ?
AnsweredDear 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...
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HaplotypeCallerSpark
AnsweredHi, 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...
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BQSR Pipeline Spark
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...