Understanding File Formats in Bioinformatics: VCF and gVCF

Опубликовано: 26 Сентябрь 2022
на канале: Bioinformagician

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This is a quick video going over a very commonly used file format while performing variant calling analysis - VCF file. In this video, I will go over various fields in a VCF file while taking a look at an example VCF, understanding how the data is organized and what information do various fields store. In addition, I explain what are genotypes, difference between phased and unphased genotype, how to calculate alternate allele frequency and look at how DNA variations are recorded. Lastly, I also discuss what is a gVCF file and in what ways a gVCF file differs from a VCF file.
I hope you find this video helpful! Leave your thoughts in the comment section below!

FASTA/FASTQ format:
• Understanding Bioinformatics File For...

SAM/BAM file format:
• Understanding Bioinformatics File For...

Chapters:
0:00 Intro
0:40 What is a VCF file and how is it generated?
2:38 Main sections of a VCF file
3:27 Metadata section
5:51 Header line
6:51 Data lines - description of fields
13:13 Genes and alleles
14:30 Understanding genotype
15:33 What does genotype 2/0 or 1/2 mean?
17:02 Difference between GT:0/1 and GT:0|1 - phased vs unphased genotype
10:05 How are variants recorded in a VCF file?
22:01 Interpreting a record in VCF
24:45 Genomic VCF (gVCF)

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Website: https://bioinformagician.org/
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