User: quentin54520

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Posts by quentin54520

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Gatk spark beta
... Hello all, Do any of you have any recent info on spark versions of gatk4 tools that are still in beta? I have human genomes from which I want to identify variants causing a rare disease, so I follow the "Best practices for snp on germline". If I understood correctly to be able to multithreading wit ...
genome gatk spark written 3 hours ago by quentin545200
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Comment: C: Alignment: how to deal with read mapped on decoy
... It's whole genome sequencing from a cohort of patients. The goal is to identify the genetic causes of their rare disease ( SNV, short indel or SV). for the software: i used Bwa mem with the reference hg38 no_alt_plus_hs38d1_analysis_set. ...
written 1 day ago by quentin545200
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Alignment: how to deal with read mapped on decoy
... Hello all, I made my alignments with a human reference containing decoys. I know how to remove reads that aligned up with decoys but what I don't know is: should I do it? For the header it's the same thing, do I have to remove the @SQ lines corresponding to the decoys ? I have some reads with th ...
genome alignment written 1 day ago by quentin545200
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Alamut batch vs free annotation tools like VEP
... Hello all, we are considering purchasing an alamut batch license for variant annotation. I would like to have your opinion knowing that it is very expensive, I wonder what it really brings compared to VEP (with the use of plugin to add the effect on the splicing for example). ...
genome written 6 days ago by quentin545200
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Comment: C: How to optimized the alignment with bwa mem
... Yes it's what i want to do. But for the moment it's too complicated for my knowledge... But of course i planned to learn how to used snakemake. ...
written 7 days ago by quentin545200
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Comment: C: How to optimized the alignment with bwa mem
... Thanks. And so when i use an sbatch array, in the sbatch option i could put #sbatch --cpus-per-task=18 to obtained 18 cpu for each jobs (so as i request 10 maximum simultaneous jobs, whit this option i request a maximum of 180 cpus ?) And in this case i could add something like --mem-per-cpu=1000 t ...
written 7 days ago by quentin545200
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How to optimized the alignment with bwa mem
... Hello all, I need to do alignment of 74 human genome (it's 30x genome). For each i have 8 files because they were sequenced on 4 differents lane and it's paired end data. To do these 296 alignments i thinks that job array is the best option to parallelize. But i'm not sure how to do that. On the ...
genome alignment bwa written 7 days ago by quentin545200
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Tools for structural variant on exome
... Hello all, Do you know good tools for structural variant calling on exome sequencing data ? It's human exome for germline variations. I know some tools for genome but i don't thinks that it's good for exome... Thanks ...
exome sv structural variant sequencing written 12 days ago by quentin545200
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Comment: C: Human WGS :which genome reference
... Even [the GATK article][1] is not really up to date as it used the gatk 3... Maybe as i don't know which genome used, is better tout used the no alt to be sure even if i will miss some intersting future about alt contig. [1]: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How- ...
written 16 days ago by quentin545200
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Comment: C: Human WGS :which genome reference
... Thanks. But again it's an article from 2017. And he write to use the no alt version because the tools are not aware. But now the tool like bwa mem are alt aware... It's really dificult to found a recent source. ...
written 16 days ago by quentin545200

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