Quentin Chartreux
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Recent activity by Quentin Chartreux Sort by recent activity-
Yes I'm pretty sure the problem is with the joint genotyping step. So your recommandation is perform haplotypecaller in single sample, perform hard filtering and then merge the vcf to obtain a mul...
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Genevieve Brandt (she/her) I see that i have two Time the same variable name in different commands that didn't mean the same things. For the dragmap command REF_genome is the path to the direc...
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Hi Genevieve Brandt (she/her) I will try to be as precise as possible. I used the following tools: Dragmap: 1.2.1 Gatk: 4.2.3.0 I have a family with parents and 2 children. File used for some com...
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Pamela BretscherBretscher thanks you for the correction. Just to be more precise, i try this reference with these 3 files. But at the end i get a bam file with a lot of regions with read with MA...
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Actually what is very surprising is that if I use dragmap to create the hash table myself from the reference and the alt-mask.bed I get more than these 3 files.
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First of all, congratulations on all of this work. I have tested the pipeline (actually not really as a pipeline, but the commands are the same) and it is clear that the results are excellent! My m...
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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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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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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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Other question : The dragen mode of haplotypecaller can (should ?) Be use for variant calling on rna seq data ?