Understanding VCF file | Variant Call Format Part 1/3

[@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.

[@tethpheak6745]

Thank you so much for your kind sharing

[@HaileG-2020]

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

[@jinayenamin6676]

This was very helpful. Thanks :)

[@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!

[@chesterhung6154]

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.

[@sketchgamma]

Thanks dude

[@kadidyasmine8775]

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

[@LiquidBrain]

Are you looking for fastq? I usually look at SRA for those raw data

[@taniadas3301]

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

[@Dezzy7model]

probably late but for R use vcfR package.

[@chaofang9576]

great，are you malaysia？

[@LiquidBrain]

Yap, I am Malaysian

[@chaofang9576]

@@LiquidBrain thank you for your video ，later maybe you will introduction gatk？

[@marwanmahmoodsaleh8088]

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

[@LiquidBrain]

that really depends where you submitting to, is it SRA?

[@marwanmahmoodsaleh8088]

@@LiquidBrain I want to registr this sequence. May be SRA or others that can you guide me.