Excellent work!! What makes this young lady standout is that she started with raw data and showed every step in clear terms. I have seen many "tutorials" and almost all started with munged data without showing what was done and how it was done leaving the beginner at a loss. Highly commendable work!
Thank you for creating such an informative video on variant calling using GATK. As someone new to bioinformatics, I found your step-by-step explanation of the workflow incredibly helpful. I appreciate you sharing your knowledge and expertise in such a clear way. Thanks again for generously sharing your expertise!
Oh my god! You are awesome. Tu eres la mejor. You are the best. I have found finally someone who can explain the theory of what needs to be done, then do it on the command line, and then explain the reason why to use the terms. The pace is good but I also agree and I would like to suggest to give a bit of time to see what is written in the Terminal. I learnt so much from you in the past two days for watching your videos on GATK variant calling and analysis than the past two years trying to do it by myself. You make writing a script so easy, with explanations along the way. Please, keep doing these types of tutorials, so we can all benefit from these great tutorials. They make my life easier. My next tutorial with you in on RNA-seq. I already have done STAR, which it will be nice if you can do a tutorial, but if you think the way to go is HISAT2 then I am with you. Any tutorial on HISAT-3N soon on your channel? also it will be nice to explain how to install HISAT-3N step by step. I am still in the limbo with this one.
This is high quality content! Very helpful and crystal clear! Thanks so much! I was wondering... could we use fastp instead of fastqc ? since i think you can also trim with fastp if needed...is that correct? Again, thank you for this content, it is magical 😀
Hi, great information content in the video, just one suggestion, could you use some pointer or animations at each step so that it become interactive and keep track where you are talking. Thanks
Great tutorial, the best I’ve seen. I just had one quick question, what if I don’t have a known variants file to perform base quality recalibration? Should I just continue with the next steps using the deduplicated bam file? Hope you can help me with this, in any case, Thanks for the magnificent overview
Hello, I am having a serioud problem. I am performed your video content from start to finish. However, when performing fastqc step, I constantly get an error that the middle line didn't start with + for the SRR062634_2_filt.fast.gz file. Then, instead of performing this step on the command line, I did this step manually in the fastqc tool, the proces was completed but this time it gave an error in the base sequence quality of the SRR062634_1 file. So I couldn't get the same fastqc results as you. I continued to perform the steps, but after alignment, I could not get any result in the samtools view and flagstat steps. Could you please help me solve this problem? I would also like to thank you for preparing such a nice content.
Hi, thank you so much. Can you please make a video about how to compare two or more vcf files? e.g I want to extract variants that are different in sample vs group
Excellent video!! how do you run GATK for poliploid data which variant calling was made using Freebayes? how do you extract several different haplotypes from this kind of data? Thanks
Thanks for this very informative tutorial! I am trying to run the bwa index reference step, and it looks like it is stuck on the "[bwa_index] construct SA from BWT and Occ ..." step. How long does this step usually take to run?
depends on the computational power you have and the size of the reference genome... For a human reference genome, it usually takes between 30min to 1 hr
does base Qulity recalibration step is very important? beacuse, I am using this pipeline on WGS of sorghum data set. Now I have called the variants without this step ( filtering is done). I used the same vcf file for BQSR step and for some odd reason.. in my .g.vcf file there are no SNPs at all.....
Thanks a ton for putting up this video.. Could you please make videos on bi-sulfite sequencing data analysis and also chip-seq data analysis? Thanks in advance :)
Hello, you are doing a great job, but putting the command in the terminal do it a little bit slow so we can get it easily. hope you understand my point.
Hi, thanks so much for your video. When I run HaplotypeCaller I get the error "Unable to trim uncertain bases without flow order information" and I cannot find anything on the GATK website. My .bam files are validated... I was wondering if you happen to know how to solve this problem. Thanks!
Thank u foe the explanation ❤ i have a question , if i m using GATK to detect snps in virus , the.BQSR from GAtK resources bundle i use the one for human or for the virus , cause i didn't find anything on the GATK web site
Haplotype caller is taking more time, is there problem, i am using GATK 4.0, its going through each chromosome and position, i have 32 GB system though, its more than 3 hours and still have not finished process of till chromosome 2 of one whole genome
There are some tweaks you'd have to do for WES data. Check out this thread: gatk.broadinstitute.org/hc/en-us/community/posts/4411453286811-Is-there-different-pipelines-between-WGS-variant-calling-and-WES-variant-calling-
This is really helpful thank you! Your videos are amazing. Unfortunately, I am having trouble getting CreateSequenceDictionary to work. saying :Neither file nor parent directory exist
At 37:27, you did not use the $ sign with the variable data "{data}/recal_data.table". will this variable work without using the $ sign? Can you tell the difference between using HaplotypeCaller for One sample Nad Using HaplotypeCaller with -ERC gVCF mode. And when to use which one?
GATK recommends to run Haplotype caller in GVCF mode when you are running more than one sample. With just one sample, running HaplotypeCaller as normal should be sufficient.
It is great work.... its great to watch..... would you please also make a video for 3000 rice genome project and to explain how we can perform SNP variation/haplotype variation within the 3000 rice lines (not just compare two one line with the reference). I also want to perform haplotype analysis for my target gene using 3000 Rice genome project and want to check the haplotype diversity within 3000 rice lines. Anyone have some idea on it..... i would appreciate if someone can help me out
Excellent work!! What makes this young lady standout is that she started with raw data and showed every step in clear terms. I have seen many "tutorials" and almost all started with munged data without showing what was done and how it was done leaving the beginner at a loss. Highly commendable work!
Thank you for creating such an informative video on variant calling using GATK. As someone new to bioinformatics, I found your step-by-step explanation of the workflow incredibly helpful. I appreciate you sharing your knowledge and expertise in such a clear way. Thanks again for generously sharing your expertise!
Oh my god! You are awesome.
Tu eres la mejor. You are the best.
I have found finally someone who can explain the theory of what needs to be done, then do it on the command line, and then explain the reason why to use the terms. The pace is good but I also agree and I would like to suggest to give a bit of time to see what is written in the Terminal.
I learnt so much from you in the past two days for watching your videos on GATK variant calling and analysis than the past two years trying to do it by myself.
You make writing a script so easy, with explanations along the way.
Please, keep doing these types of tutorials, so we can all benefit from these great tutorials. They make my life easier.
My next tutorial with you in on RNA-seq. I already have done STAR, which it will be nice if you can do a tutorial, but if you think the way to go is HISAT2 then I am with you.
Any tutorial on HISAT-3N soon on your channel?
also it will be nice to explain how to install HISAT-3N step by step. I am still in the limbo with this one.
It would be very nice if you can also provide somatic variant analysis workflow
Was waiting for this tutorial since so long 🥺
Many many thanks!. You are helping a lot of folks out there. 😀
It would be great if you could please make another part to make the publication ready graphs and stuff like annotations from the raw vcf file
Thanks for suggestion!
You are helping a lot ! Thank you so much 🤗
Great video! Thank you very much. I'm starting to work on this field, this video helped me a lot.
hey! you are really helping a lot ! Thaaaank you so much!
Very helpfull and informative, thank you!
Amazing tutorial! Thank so much for your work!
Thanks, madam, I am waiting for this tutorial!
You are doing a great job ma'am.
That was really helpful 😊👍
This is high quality content! Very helpful and crystal clear! Thanks so much!
I was wondering... could we use fastp instead of fastqc ? since i think you can also trim with fastp if needed...is that correct?
Again, thank you for this content, it is magical 😀
I haven't used fastp before. If it does the same thing as FastQC and allows you to perform trimming as well, then go for it.
Thank you Bioinformagician ma'am
you are really helping a lot ! Thaaaank you so much!
Excellent Video Ma'am 👍
Hi, great information content in the video, just one suggestion, could you use some pointer or animations at each step so that it become interactive and keep track where you are talking. Thanks
Great tutorial, the best I’ve seen. I just had one quick question, what if I don’t have a known variants file to perform base quality recalibration? Should I just continue with the next steps using the deduplicated bam file?
Hope you can help me with this, in any case, Thanks for the magnificent overview
did you figure this out?
Perfect. Good job.
Hello, I am having a serioud problem. I am performed your video content from start to finish. However, when performing fastqc step, I constantly get an error that the middle line didn't start with + for the SRR062634_2_filt.fast.gz file. Then, instead of performing this step on the command line, I did this step manually in the fastqc tool, the proces was completed but this time it gave an error in the base sequence quality of the SRR062634_1 file. So I couldn't get the same fastqc results as you. I continued to perform the steps, but after alignment, I could not get any result in the samtools view and flagstat steps. Could you please help me solve this problem? I would also like to thank you for preparing such a nice content.
❤❤❤ Thanks You for This learn 👌💪🙏
Thank you dear
😊
Amazing amazing
Hi, thank you so much. Can you please make a video about how to compare two or more vcf files? e.g I want to extract variants that are different in sample vs group
Thanks for the suggestion, will surely plan a video on it.
Thanks so much 🌸
Excellent video!! how do you run GATK for poliploid data which variant calling was made using Freebayes? how do you extract several different haplotypes from this kind of data? Thanks
Thanks for this very informative tutorial! I am trying to run the bwa index reference step, and it looks like it is stuck on the "[bwa_index] construct SA from BWT and Occ ..." step. How long does this step usually take to run?
depends on the computational power you have and the size of the reference genome... For a human reference genome, it usually takes between 30min to 1 hr
I have a question, does this work demo needs can be run in a 16gb ram computer??'
Thank you very much for this wonderful explanation!! I have a question: can I identify CNVs in exome sequencing? I love your videos!
Hi, could you upload GWAS tutorial videos please.......
nice . SO do you have a complete pipeline of WGS data analysis from beginning to end . I mean from sequencing fastq data to variant calling??
does anywone else gets failed: Operation timed out. when trying to download the read ... ???
Thanks a lot :D
does base Qulity recalibration step is very important?
beacuse, I am using this pipeline on WGS of sorghum data set. Now I have called the variants without this step ( filtering is done). I used the same vcf file for BQSR step and for some odd reason.. in my .g.vcf file there are no SNPs at all.....
How long did the gatk BaseRecalibrator algorithm take to make the table? Thank you!
Can this pipeline be used for variant calling in bacterial genomes? Bacterial genome is haploid as opposed to eukaryotes
Thanks a ton for putting up this video.. Could you please make videos on bi-sulfite sequencing data analysis and also chip-seq data analysis? Thanks in advance :)
Sure, definitely have plans to make videos covering these topics :)
From where did she get the reference genome? She didn't mention anything about it. Anyone else knows?
Hello, you are doing a great job, but putting the command in the terminal do it a little bit slow so we can get it easily. hope you understand my point.
hi, could you please tell how do we remove genome duplication in our sample?
Hi! Could you please make another video on how to call germline CNV and CV or provide me a good tutorial on this topic?
Hi, thanks so much for your video. When I run HaplotypeCaller I get the error "Unable to trim uncertain bases without flow order information" and I cannot find anything on the GATK website. My .bam files are validated... I was wondering if you happen to know how to solve this problem. Thanks!
do you have any video that informs us about the prerequisites that you mentioned like the linux coding and all?
how can we set ploidy argument in GATk , can you share tge script fot that. thanks
Thank u foe the explanation ❤ i have a question , if i m using GATK to detect snps in virus , the.BQSR from GAtK resources bundle i use the one for human or for the virus , cause i didn't find anything on the GATK web site
Hi. Thanks for the tutorial, it helps me a lot! I have a question, how many GB is the resulting .sam file?
Haplotype caller is taking more time, is there problem, i am using GATK 4.0, its going through each chromosome and position, i have 32 GB system though, its more than 3 hours and still have not finished process of till chromosome 2 of one whole genome
Hi
BQSR is too slow any idea how to speed it up?
I am using GATK's latest version
thank you again for you videos. Could we apply this workflow on scRNAseq data ?
Ma'am when are you gonna upload the same stuffs for somatic mutation calling?
Hİ, thank you for tutorials. I have one question. Is there any difference wes and wgs data analysis? Can I use this workflow in wes data analysis?
There are some tweaks you'd have to do for WES data. Check out this thread: gatk.broadinstitute.org/hc/en-us/community/posts/4411453286811-Is-there-different-pipelines-between-WGS-variant-calling-and-WES-variant-calling-
How to add executable to the path?
I am using Windows for running this. Would you please tell me how to use Docker to run this commands?
GATK HaplotypeCaller runs very slow. any tips to make it work fast?
This is really helpful thank you! Your videos are amazing. Unfortunately, I am having trouble getting CreateSequenceDictionary to work. saying :Neither file nor parent directory exist
I have the same issue how did u solve it plz ?
me too, did you find a way to solve it?@@nourlarifi1689
Could you make a video on using the limma package for gpr files from GEO? It would be so helpful. Or do you do private tuition? Thanks a million!
Even I would like to attend if she conducts tuition
I will surely consider making a video using limma package and no, I do not provide private or any type of tutoring. Thanks!
At 37:27, you did not use the $ sign with the variable data "{data}/recal_data.table". will this variable work without using the $ sign?
Can you tell the difference between using HaplotypeCaller for One sample Nad Using HaplotypeCaller with -ERC gVCF mode. And when to use which one?
GATK recommends to run Haplotype caller in GVCF mode when you are running more than one sample. With just one sample, running HaplotypeCaller as normal should be sufficient.
Could you please tell... Is 16 gb ram is enough for running gatk?
Hall Patricia Harris Daniel Lopez Mary
It is great work.... its great to watch..... would you please also make a video for 3000 rice genome project and to explain how we can perform SNP variation/haplotype variation within the 3000 rice lines (not just compare two one line with the reference). I also want to perform haplotype analysis for my target gene using 3000 Rice genome project and want to check the haplotype diversity within 3000 rice lines. Anyone have some idea on it..... i would appreciate if someone can help me out
Hi, any updates on doing SNP analysis on 3000 lines?
@@mananchelvan157 no dear, still no update. Maybe this is not her area of interest. I also really need this analysis
what about SRR __ 2
?
your bases at the end are of low quality so why not trim it ?
Davis Shirley Garcia Ruth Jackson Lisa
could you help about
ancestry
really really really helpful !!!!! I succeed !!! hhhhh😘
It would be great if you could please make another part to make the publication ready graphs and stuff like annotations from the raw vcf file.
Currently working on it!