Understanding File Formats in Bioinformatics: VCF and gVCF

[@magdalineakinyi5928]

I am a bioinformatics student,just began my studies and I have really learnt a lot from your content 😊

[@abubakarraja7605]

I am beginner in bioinformatics field I have not learnt these things from my institute as compared to what amazing things I have learnt from your channel thank you so much !

[@mosesbaraza3369]

Quite explicit explanation and detailed and very chronologically arranged. Looking forward to learn in subsequent lessons

[@humarafique3093]

Really really amazinggggggg and informative video for the beginners. At 16:40 the position 491520 where the GT is 1/2, there shouldn't be C/CAC instead of CAC/C?

[@alexeyslinkin4589]

I see where your question is coming from, but in this case, the order does not really matter. The forward slash notation (1/2), as opposed to the pipe notation (1|2), indicates that the genotype is unphased. This means we don't know which alleles (C and CAC) are on which chromosome, or in other words, which allele comes from the father, and which comes from the mother. Technically, yes, based on the table, genotype 1/2 corresponds to C/CAC, and if it were 2/1, then CAC/C, but again in this case there's no difference.

[@hubijohn7451]

Am I glad I found this channel. Great stuff!

[@isadoramachadoghilardi3168]

Excellent video! I'm in love with your channel!! Congratulations!! I'm starting in this world of bioinformatics, and your videos have helped me a lot! Thank you!

[@seetarajpara7626]

I love your channel!! Your content is so well organized, thank you so much!

[@josephinecudjoe3207]

I have been blessed by your videos. Thank you.

[@yuxiang4218]

Very helpful! Thanks for sharing.

[@faezedarbaniyan1787]

Thank you so much for elaborating this. I can't relate the definition of Allele Frequency that you mentioned here for rows 2 and 3 in your sample (at 23:44 minutes). Can you please explain it for those?

[@alexandrakassis3525]

Thank you so much for sharing this information and your knowledge! Very much appreciated. Could you please make a video on doing a joint variant calling? And also, what you would do for joint calling on rna-seq data?

[@DonnchaDunican]

Thanks - great teaching.

[@Tekofilic]

Had always been looking for such a video. Thank you so much :D

[@minxie2210]

Thank you for the great video. One quick question regarding the "What does genotype 2/0 or 1/2 mean?" section. In the 4 examples you are given, should the second one be C/T instead of C/A from the genotype numbers? Thanks again, really appreciate your effort in making all the great videos!!

[@giovannapg7532]

OMG such a good video!!! You can explain everything so amazingly ❤ Could you please one day make a tutorial about data set integration on Seurat, as 10X genomic and Smart-seq2 integration??? Thank you!!

[@Bioinformagician]

Definitely have plans to make a video covering this. Thanks for the suggestion!

[@설동헌-i8d]

Such a great lecture! I am just wondering if there is a typo at 17:00, the second row of the table at 332470 position. It has to be C/T not C/A or is there anything I missed?

[@Bioinformagician]

Yes, that is a typo. It should have been A instead of T.

[@biomagician]

Absolutely fantastic video! Thank you! Does a gVCF always respect the VCF format or is there a distinct gVCF format? Can you tell us more about the multi-sample VCF formats jVCF and MSVCF? Thanks!

[@abebemisganaw7377]

exciting video. Could you upload another video about how to analyze data using VCF tools in a Linux environment

[@tapanbaral8939]

Really informative tutorial. Could you please make a video on TMB and MSI ?

[@notterboutuyer2781]

what was the name of the forum mentioned?

[@MalahatDianat]

Thanks a lot. It was very useful.

[@AshishKumar-el8sb]

If i have inserted the part of the same genome in a genome how can i find it

[@anmolpardeshi3138]

16:59 - 332470 - shouldn't that be CT or TC - since, for that position, T is reference allele (0) and C is 1st alternate allele (1) - how did you get C/A?

[@Bioinformagician]

It’s a typo. It should be T

[@anmolpardeshi3138]

@@Bioinformagician thanks for the clarification and wonderful videos. I'm trying to make such an effort too. One suggestion would be to pin such clarifications so that they are not lost in a myriad of comments.

[@alexandrakassis3525]

Where can I find your power points you use in your videos?

[@kajalpanchal8239]

everything is soo good but am i the only one who is facing sound issue? can you please consider that your sound level is really low. otherwise you are a saviour

[@Bioinformagician]

Thank you for pointing it out. I will try to maintain optimal sound levels for my future videos :)

[@AshishKumar-el8sb]

How to extract total genes from the genome files.

[@jattpigeonscorner9368]

Thank you!

[@stemcell1167]

Is there a way to get Allele frequency for each sample in multisample VCF file OR is there a way to get AO and RO .

[@sauravroy3420]

you can slit the sample using bcftools and then use it accordingly

[@sonalvishwakarma30]

I want to make a request. Could you please make videos on RepeatMasker it would be really helpful

[@nabildhifallah361]

YES IFOUND THI VIDEO HELPFULL because i can use the whole information about the chromosome and the position the single nucleotide poistion on that chromosome (ALT) compared with the reference of DNA sequence with that i can see well if i have an insertion or convertion or deletion in the dna sample .i am thanking you for your best explanation for the metadataline ,the header and the format .thank you

[@mostafaismail4253]

Can You make a tutorial on BS-seq and copy number variations (CNV)? It will be great if you did it 💛 Thanks too much .

[@mostafaismail4253]

Really you are life saver for my tasks.

[@Bioinformagician]

Thanks for the suggestion, I will surely consider covering these topics in future videos :)

[@njagimwaniki4321]

How can a VCF record exist where the genotype is 0|0 ? Doesn’t that mean that both the chromosomes match the reference?

[@AshishKumar-el8sb]

chrM what it denotes

[@vinaydeep26]

is the position of the variant with respect to the chromosome? or the whole reference? if there is chr 20 position: 1000 does it mean the variant is from the start of the reference or the chromosome?

[@Bioinformagician]

Position on the chromosome

[@MuhammadFaizan-mi9yo]

I have a very seruious query that got stuck at a point due to which all my projects are halted and I know you can answer my query. if you are willing to help plz reply I will post my query madam. I would be obliged to you plz take this as a request

[@jeetnanshi4357]

Im sorry but the tone is very monotonus. use a marker or please take a break :(