Quentin Chartreux
- Total activity 57
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 0
- Subscriptions 16
Activity overview
Latest activity by Quentin Chartreux-
Quentin Chartreux commented,
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...
-
Quentin Chartreux commented,
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 directo...
-
Quentin Chartreux commented,
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 comma...
-
Quentin Chartreux commented,
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...
-
Quentin Chartreux commented,
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.
-
Quentin Chartreux created a post,
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...
-
Quentin Chartreux commented,
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...
-
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} ...
-
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...
-
Quentin Chartreux created a post,
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...