Consider this minimal VCF file which contains a multi-allelic call made by a somatic variant caller on a human tumor sample: ``` ##fileformat=VCFv4.3 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic …

I'm new to genomics platform. When I was analyzing the alignment data in IGV i came across the word "Pair Orientation"with values "F1R2", "F2R1". I …

I'm doing variant calling using GATK4's Mutect2 and trying to filter variants based on strand bias and other metrics and I feel like the F1R2 …

Hi all, I'm trying to pull strand count information from a VCF file made using GATK4's Mutect2. I used the following command to create this …

I have 4 columns in my annotated VCF "FATHMM_SCORE, FATHMM_PRED, FATHMM_MKL_CODING_SCORE, FATHMM_MKL_CODING_PRED". Can someone please explain what is the difference between these two scores?

I am new to bioinformatics and trying to understand the zygosity of variant/allele in VCF data. Couldn't find proper bioinformatics explanation anywhere, can someone please …

I'm looking at one of my VCF files and I noticed that allele depth (AD) isn't just one number, but rather two values seperated by …

Hi, I'm working with some RNA-Seq data, and I have created my bed files. When I run bedtools coverage, the output has 16 columns. I …

Hello I am having some trouble interpreting the pv4 values I get in my .vcf files I know that pv4 field shows: PV4: P-values for …

Hello all, I am analyzing the variant call analysis from my** identical twins**. (they are confirmed as having a same disease-causing mutation, which was a …