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To find overlapping variants between two files, you can use bcftools. If you want to generate a simple venn diagram, you can provide lists to http://bioinformatics.psb.ugent.be/webtools/Venn -
filtering variants with R
Hi,
I'm learning data analysis with R, using RStudio.
I have my data in one file. I have variants from 3 tissue types, from 130 individuals. I would like to filter the variants within each individual, so that I can get: 1. unique variants for all 3 tissues, 2. variants common to all tissues, 3. variants common between 2 tissue types.
The file that I'm working on has 118 columns (vcf annotated file), I would like to keep all columns.
I've tried VennDiagram package, but it filters out variants that are present in any other individual, so in the overlapping files I loose some variants.
I understand that I would need to use loop filtering, so that 1. I pick individuals by "ID" column, then sort variants by "variant" column and compare them between "tissue" column to output into all filtered types of variants (unique and common).
Does anyone know how to do that???
Cheers,
A.
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Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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