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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
• December 04, 2021 10:08
• 4 followers
• 12 comments
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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
• November 23, 2021 10:42
• 2 followers
• 5 comments
• 0 votes

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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
• October 22, 2021 09:41
• 2 followers
• 6 comments
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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
• September 10, 2021 12:27
• 4 followers
• 14 comments
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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
• August 25, 2021 13:11
• 2 followers
• 1 comment
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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
• July 19, 2021 12:58
• 2 followers
• 2 comments
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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
• July 13, 2021 15:19
• 2 followers
• 3 comments
• 0 votes

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
• May 24, 2021 10:47
• 3 followers
• 6 comments
• 0 votes

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
• April 01, 2021 09:06
• 2 followers
• 1 comment
• 0 votes

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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
• March 30, 2021 09:42
• 2 followers
• 3 comments
• 0 votes