User: deniselavezzari

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Posts by deniselavezzari

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Comment: C: Supplementary aligments in VAF
... Thanks, I was wondering if there is a "general rule" indipendent from the variant calling. ...
written 24 days ago by deniselavezzari0
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Supplementary aligments in VAF
... Hi everyone! I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot, ...
genome frequency alignment snp sequencing written 24 days ago by deniselavezzari0
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SNP index definition
... Which is the definition of SNP index? Someone asked me to calculate the SNP index, but I cannot find a definition. ...
next-gen alignment sequencing written 11 weeks ago by deniselavezzari0 • updated 11 weeks ago by ahmad mousavi520
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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 8 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 8 months ago by deniselavezzari0 • updated 8 months ago by Ram32k
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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 11 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 11 months ago by deniselavezzari0 • updated 11 months ago by GenoMax96k
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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 12 months ago by deniselavezzari0 • updated 11 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 12 months ago by deniselavezzari0 • updated 12 months ago by ATpoint46k

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