Bioinformatics101 - What is a VCF File?

[@kingbx00]

this video is really helpful, thank you

[@mostafarahman5394]

can you please make a video how to convert a VCF SNP information into a binary data for population strcuture or phylogentic analysis?

[@fatimaejaz937]

Yes, and how we can use vcf files to see what genes in the reference genome the variants correspond to.

[@sprucemoose1133]

Thank you! Great video!

[@elenips7231]

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!

[@bioinformatics1015]

Hi! Do you have access to the BAM files for each sample? The analysis you describe typically involved passing the two BAMs (tumor & healthy) into a variant caller like Mutect2. I will place the link to the tool below:
gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

[@GCSRaji]

thank you for sharing this..... i have a question regarding this topic....how to put command in VCF and BCF tools.. can you make a demo for this?

[@shado7120]

Thank you

[@GCSRaji]

@@shado7120 .. for What?

[@wholegirma1220]

Thank you sir

[@mes2587]

Well explained, thank You!

[@annap1239]

Thank you. it was useful

[@srishtikushwaha6475]

Thanks a lot

[@waveoflight]

Acronyms are ridiculous.