User: deniselavezzari
deniselavezzari • 0
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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
deniselavezzari • 0
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... Hi everyone!
I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated?
Thanks a lot, ...
written 24 days ago by
deniselavezzari • 0
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... Which is the definition of SNP index?
Someone asked me to calculate the SNP index, but I cannot find a definition. ...
written 11 weeks ago by
deniselavezzari • 0
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11 weeks ago by
ahmad mousavi • 520
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... 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 ...
written 3 months ago by
deniselavezzari • 0
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C: Multiple VCF filtering
... Thank you very much. ...
written 8 months ago by
deniselavezzari • 0
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... 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 ...
written 8 months ago by
deniselavezzari • 0
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8 months ago by
Ram ♦ 32k
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... Hi,
are there any suggestion for the filtering of the consensus reads created?
Thank you,
...
written 11 months ago by
deniselavezzari • 0
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... 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 ...
written 11 months ago by
deniselavezzari • 0
• updated
11 months ago by
GenoMax ♦ 96k
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... 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 ...
written 12 months ago by
deniselavezzari • 0
• updated
11 months ago by
Biostar ♦♦ 20
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... 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 ...
written 12 months ago by
deniselavezzari • 0
• updated
12 months ago by
ATpoint ♦ 46k
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