User: Leandro Batista
Leandro Batista • 100
- Reputation:
- 100
- Status:
- New User
- Location:
- Paris
- Last seen:
- 8 years, 3 months ago
- Joined:
- 8 years, 7 months ago
- Email:
- r**************@gmail.com
Posts by Leandro Batista
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... Hi everyone,
I'm calling SNPs with UnifiedGenotyper:
java -Xmx2g -jar /Volumes/DroboLeandro/Analysis/Software/GenomeAnalysisTK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /Volumes/DroboLeandro/Analysis/Genomes/Reference/NCBIM37.chr.fa -I BALBcByJ.recal.bam --dbsnp /Volumes/DroboLeandro/Analysis/db ...
written 8.5 years ago by
Leandro Batista • 100
• updated
4.8 years ago by
fufuyou • 110
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... Hello,
I've been using GATK tools for Bam processing and SNP calling in whole exome and whole genome sequencing data. It has been doing just fine on several samples.
Today, unexpectedly, when running CountCovariates, some gave an error it had never given before. I've searched on the internet, but ...
written 8.5 years ago by
Leandro Batista • 100
• updated
8.5 years ago by
Pierre Lindenbaum ♦ 130k
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... My understanding is that SomaticIndelDetector only makes that difference (germline/somatic indel) when analyzing two samples (tumor and normal). In the unpaired mode, I guess it just calls Indels... ...
written 8.5 years ago by
Leandro Batista • 100
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... Hey Guys,
I've been establishing my own first pipeline for calling variants: Indels and SNPs. For that, I used mainly GATK tools.
I'm doing this for whole genome and whole exome sequences of mouse inbred strains.
So I'd like to hear your opinion about calling Indels with SomaticIndelDetector ( ...
written 8.5 years ago by
Leandro Batista • 100
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Comment:
C: Markduplicates Error
... Thanks for your answers. I think it worked when setting VALIDATION_STRINGENCY to LENIENT. Anyway I don't understand why I'm having this problem. I'm using Bam files aligned and produced by Sanger Institute and I'm processing them on my own pipeline to call SNPs. Steps leading to Bam file production ...
written 8.5 years ago by
Leandro Batista • 100
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... Hello,
I'm processing whole genome BAM files. Since I'm specifically interested on chromosome 11, I have split my files and I'm working only on this chromosome. However, when I tried to run MarkDuplicates on chr11 bam files, it gave the following error:
SAM validation error: WARNING: Record 23, R ...
written 8.5 years ago by
Leandro Batista • 100
• updated
7.3 years ago by
Biostar ♦♦ 20
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... Still considering this question of Training set, do you use the Sanger VCFs as truth sites or just training? ...
written 8.5 years ago by
Leandro Batista • 100
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... Although not mouse specific, I'd say that PosMed is a great resource for positional cloning and other candidate gene approaches:
http://omicspace.riken.jp/PosMed/ ...
written 8.5 years ago by
Leandro Batista • 100
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... To overcome that, I was thinking to repeat the SNP calling on all the strains I'm using to compare. That way I would follow the exact same steps and parameters for each data. ...
written 8.5 years ago by
Leandro Batista • 100
0
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... There's no problem in converting this file. I just wanted to know if there was another way or another files. I just received the whole-exome sequence for 1 strain and our goal is to call variants, specially SNPs and compare it to some other strains completely sequenced in the Sanger's mouse project, ...
written 8.5 years ago by
Leandro Batista • 100
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