Hello everyone, I'm currently using CIBERSORTx to create a new matrix for my single-cell RNA-seq dataset. I aim to use CIBERSORTx to generate a reference, …

hello everyone, I got a vcf file with variation called using hg38 as reference genome. I wonder what would happen if I use hg19 as …

I'm trying to annotate variants in a vcf file according to: - position - variant type My bcftools command looks something like this: bcftools annotate …

Hi all, I have been doing variant calling of somatic variants in exome seq of human genome using GATK pipeline based preprocessing and VarDict variant …

Hi all! First time analyzing WES, wanted to make sure downloading the best suited reference fasta file. In the mouse gencode site (https://www.gencodegenes.org/mouse/release_M25.html) I saw …

Hello, I have a vcf file which consists of mutations that was generated using the GATK variant calling workflow. For this the `hs37d5` assembly was …

hello everyone , I am analyzing fastq files on galaxy. I aligned fastq files to hg38 reference genome using `bowtie2` and produced `BAM` files. now …

Hi everyone, I am new to PLINK and trying to understand it as I go. I currently have a list of ~6100 variants and would …

Hello I am human reference genome in .gz format "Homo_sapiens.GRCh38.dna.toplevel.fa.gz" . I need to create its .gzi index to load reference genome. Can anyone guide …

<p>Hello everyone- Im trying to set up a pipeline in GATK for variant analysis. I have human whole genome data, exome data and transcriptome data. …