User: deniselavezzari

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Posts by deniselavezzari

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Best way to deal with chimeric reads?
... Hi everyone! I have some DNA data (custom panel on human gene) that have a lot of chimeras reads, due to the library preparation procotol. I have aligned the data with BWA and then call variants with GATK HC, but I was wondering if there is a better way to align the chimeric reads and call variants ...
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Comment: C: Multiple VCF filtering
... Thank you very much. ...
written 4 months ago by deniselavezzari0
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Multiple VCF filtering
... Hi! I have a vcf with 20 samples and I want to remove from it the variants that are commons (with the same zygosity) to all samples. How can I do it? Thanks ...
vcf wgs exom illumina written 4 months ago by deniselavezzari0 • updated 4 months ago by RamRS30k
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Comment: C: How to take in consideration UMI in WES pipeline?
... Hi, are there any suggestion for the filtering of the consensus reads created? Thank you, ...
written 7 months ago by deniselavezzari0
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How to analyze DNA data with UMI
... Hi all! I'm facing with analyze DNA exomes sequencing data with UMI. From the demultiplexing, I have three fastq files: one for reads R1, one for the UMI tags, and one for the R2. Now, I have to align data to the reference genome and call variants. Have you some suggestions for me? Does anyone know ...
bioinformatics umi next-gen sequencing written 8 months ago by deniselavezzari0 • updated 8 months ago by genomax92k
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VCF comparison: shared variants
... Hi! Is there a way to compare two vcf not only by position, but also for the genotypes? I want to extract from two vcf files the variants shared by both individuals, having not only the same position but also the same genotype. Thanks ...
genome snp sequencing written 9 months ago by deniselavezzari0 • updated 7 months ago by Biostar ♦♦ 20
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BWA MEM paramenter
... Hi everyone! I have a question about BWA-mem parameters. I know that is usually better to use default ones, but I want to know if someone try to change one or more of them and what are the consequences of changing one of these parameter and if there are some case in which is better to change it and ...
forum alignment sequencing written 9 months ago by deniselavezzari0 • updated 9 months ago by ATpoint41k
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Comment: C: Create a gold standard
... This article is very interesting, but what I would like to do is to create a Vcf gold standard from the same individual for which I have the genome and many exomes done with different kit and platform. I want to create it in order to use it for variant calling software comparison. Is there any artic ...
written 15 months ago by deniselavezzari0
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Create a gold standard
... Any suggestion to create a gold standard for an individual using all exomes/genome sequencing available? ...
genome written 15 months ago by deniselavezzari0

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