Understanding VCF file | Variant Call Format Part 1/3

Variant Call Format is a text file that contains information of the "Variants" between the references genome and the sample genome. It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. The format also has the ability to contain genotype information on samples for each position

It was used extensively during the 1000 human genome projects for GWAS analysis and was included in many bioinformatics research pipeline. Yet, most researchers are having problems understanding how this file can be read directly and be used in their analysis.

In this 3 part videos, I am going to go through the whole specification of the .vcf file format. The metadata section, data section, and some examples to check if your understanding matches mine.

Link to slides

Original specification file

Sample vcf

[maraoz]

I've been lost trying to understand differences between FASTA, FASTQ, VCF, and CRAM for some days now, and I finally get it. thanks for this video!

[emetitiri]

Really appreciate this series, thanks! Your descriptions are clear and easy to understand.

[elenips]

Very helpful video, thank you!!  I am not really familiar with bioinformatics and in this part of my project, I am trying two compare two VCF files corresponding to the results of healthy tissue and tumor tissue. I want to compare these VCF files and remove their similarities. More specific I want to remove the information of the healthy tissue from the tumor one. Have you any suggestions on which tool I should use or any way that I can do my analysis? thank you in advance!

[kadidyasmine]

Hello

Am currenly working on a theme: use of neural network to identify somatic variations, i would ask you if u have an idea from where can i get suitable dataset
Thank you

[HaileG-]

How to convert numerical GT format to letter or nucleotide GT format???

[taniadas]

Any tutorial on how to parse a vcf file in python\ R?

[chesterhung]

How about translocation? Translocation is another form of structural variation where non homologous chromosomes break apart and rejoin back to each other chromosomes by DNA repair machinery.

[marwanmahmoodsaleh]

Hello
I had done the whole genome sequence by NGS (Illumina) of the bacteria. The files I received from the company are Fastaq1, Fastaq2, Filtered 1 Fastq Filtered 2 Fastq and analysis results file include :rmdup.bam.bai, rmdup.bam, filtered vcf and annotated vcf. Please tell me which of these files should be converted to FASTA and submitted to NCBI? Thanks