Amazing videos, crisp and worth the time invested watching. Solution to KCQ 5 is as below: POS : 2 REF : TCG ALT1 : TG - {Deletion of C at position 3} ALT2 : T - {Deletion of C and G at position 3 and 4 respectively} ALT3 : TCAG - {Insertion of A at position 4, which pushes G from position 4 to position 5}
Hello, thank you for your efforts, it is well explained. For the C-->G, it is a transversion, because C and G do not belong to the same family ( C is pyrimidine and G is a purine ).
Why wouldn't example 3 (t=3:50) have the POS=3, REF=C, and ALT=CA instead? Wouldn't that be the same but more efficient? Great set of videos by the way 👌
It was displayed as two/three digit since the position was on 2, and thus the REF and the ALT is displayed as that. To be honest I am not really sure why it was design this way, and different libraries sometimes do something different with their output. but both method of representation actually describe the same outcome.
I am working with a vcf file and am looking for information on how missense and nonsense data is represented without going to the summary html. Could you point me in the right direction?
Not sure what would be your down stream analysis on the vcf, but maybe have a look at the vcftools (vcftools.sourceforge.net/), or there's a lot of tools available in the Galaxy.org (usegalaxy.org/) (VCFfilter) to get the statistics around the the vcf data. I am not exactly how to do it, but do email us at liquidbrain.r@gmail.com and I can see what i can do
Thank you very much, Sir. Can you share the bash script for genomic variant format (GT) conversion from 0/0, 0/1, 1/1, ./. to 0, 1, 2, and NA, from 0, 1, 2, and NA to letters/nucleotide bases (diploid form: AA, CC, GG, TT) or directly from 0/0, 0/1, 1/1, ./. to letters/nucleotide bases (diploid form) and vice versa. I think these are the backbone for any downstream data analysis, and I am also facing many problems related to those. The script for file form and genomic variance conversion (GT) may be also in R script or Python script. Waiting for your kind response.
Great explanation, would you explain how ref and alt alleles are assigned in a vcf file. Is it assigned on the basis of allele frequency? As in a larger population there may be different types of snps such as A, C, T, G, then how only one snp is assigned as Alt allele? Is it assigned on the basis of its frequency in the population? E.g In different individuals of a population, there may be many possible snps at a specific position such as A, T, C, G. So who can we know that which snp could be the Alt allele?
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!
Hi! I was wondering if is it possible to create my own .vcf file? If it is, how do you create one? Because I have my genotypic data with SNP data but in .csv file. I need to convert it to vcf file to use it for GWAS. I do appreciate if you can answer this. Thank you.
For vcf you can generate them from the bam file after you mapping step, there's a great guide here from EMBL's European Bioinformatics Institute :) www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf
Amazing videos, crisp and worth the time invested watching.
Solution to KCQ 5 is as below:
POS : 2
REF : TCG
ALT1 : TG - {Deletion of C at position 3}
ALT2 : T - {Deletion of C and G at position 3 and 4 respectively}
ALT3 : TCAG - {Insertion of A at position 4, which pushes G from position 4 to position 5}
But why are these 3 different mutations not listed as separate lines of the VCF file? Why separate them by commas on the same line?
great couple of videos. Very helpful
Thank you! The videos are super insightful and helpful! Keep up the awesome work!
Thanks a bunch! It helped me greatly in my work :)
Thanks for the videos. Very informative for my next job interview!
Hello, thank you for your efforts, it is well explained. For the C-->G, it is a transversion, because C and G do not belong to the same family ( C is pyrimidine and G is a purine ).
Thanks for posting this, mutation naming scheme is confusing 😅😅
transitions (AT or GC) or transversions (AG, AC, GT or CT)
This is super helpful! Subscribed :)
Hello. where can i check the answer? i did not find it :( .. thank you very much
Thank you for this making this video
Nice video. Please keep going. Thank you very much.
Hey Brandon -- could you update the slides link please?
How we can split VCF files from single VCF file and how we convert single VCF file to pfam format and how we can use plinkseq ?
Why wouldn't example 3 (t=3:50) have the POS=3, REF=C, and ALT=CA instead? Wouldn't that be the same but more efficient?
Great set of videos by the way 👌
Do VCF's then not necessarily use the most efficient way of reporting then?
It was displayed as two/three digit since the position was on 2, and thus the REF and the ALT is displayed as that. To be honest I am not really sure why it was design this way, and different libraries sometimes do something different with their output. but both method of representation actually describe the same outcome.
I am working with a vcf file and am looking for information on how missense and nonsense data is represented without going to the summary html. Could you point me in the right direction?
Not sure what would be your down stream analysis on the vcf, but maybe have a look at the vcftools (vcftools.sourceforge.net/), or there's a lot of tools available in the Galaxy.org (usegalaxy.org/) (VCFfilter) to get the statistics around the the vcf data.
I am not exactly how to do it, but do email us at liquidbrain.r@gmail.com and I can see what i can do
Thank you very much, Sir.
Can you share the bash script for genomic variant format (GT) conversion from 0/0, 0/1, 1/1, ./. to 0, 1, 2, and NA, from 0, 1, 2, and NA to letters/nucleotide bases (diploid form: AA, CC, GG, TT) or directly from 0/0, 0/1, 1/1, ./. to letters/nucleotide bases (diploid form) and vice versa. I think these are the backbone for any downstream data analysis, and I am also facing many problems related to those. The script for file form and genomic variance conversion (GT) may be also in R script or Python script. Waiting for your kind response.
Great explanation, would you explain how ref and alt alleles are assigned in a vcf file. Is it assigned on the basis of allele frequency? As in a larger population there may be different types of snps such as A, C, T, G, then how only one snp is assigned as Alt allele? Is it assigned on the basis of its frequency in the population? E.g In different individuals of a population, there may be many possible snps at a specific position such as A, T, C, G. So who can we know that which snp could be the Alt allele?
Example 5 mutation is called "Translocation"
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!
Hello, I have a VCF file, but I am not sure how to open it. Do you have an advice?
Hi, how big is the file? Small file can open in notepad directly, if it is too large you can try to use galaxy to process the file and view from.there
Nice lecture big thanks. Could you pls make a video on analysis using tablet
I can try 🤔
Hi! I was wondering if is it possible to create my own .vcf file? If it is, how do you create one? Because I have my genotypic data with SNP data but in .csv file. I need to convert it to vcf file to use it for GWAS. I do appreciate if you can answer this. Thank you.
For vcf you can generate them from the bam file after you mapping step, there's a great guide here from EMBL's European Bioinformatics Institute :)
www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_AgriOmics/dan_bolser_snp_calling.pdf
Nice tutorial!
Thank you so much! It is useful for me job interview~
Best of luck!
thank you
thank youuu