WGS Variant Calling: Variant Filtering and Annotation - Part 2 | Detailed NGS Analysis Workflow

[@julinha_87]

I usually never comment on anything, really, but I would be remiss if I didn't mention what a great job you are doing. There are not a lot of videos, or at least none I could really find, that make video tutorials on such specific topics like this. Really good job :) Thank you!

[@silvereyes000]

Yes I actually struggled really much to find just one more video on this topic. kzbin.info/www/bejne/o3zUlZmaqdtjmassi=7zbH49Ud9JGeXiMH You can refer this too. But the tutor is an African. So you may find his accent a bit difficult. But this is also a good video. I watched both

[@eyadelbahtety2111]

Both videos part 1 and 2 are incredible, thank you so much for your dedication and hard work putting this together in such good details. You have helped me significantly understand how to utilise this workflow to process bam files all the way into my variants of interest. Thank you!

[@belizg1]

Thank you very much for Part 2 and especially for focusing on hard filtering as we requested you to do the video

[@415chung]

Fantastic! Your presentation is clear and detail, helps me a lot in understanding the hard filtering process😊

[@hayatdeen]

i wish i found you sooner, i had to painstakingly browse though tones of GATK web pages to get me started with the Best practice guidelines. you made it clearer

[@harshasatuluri4540]

Thank you ma'am for sharing ur knowledge.... Happy to be ur student form online😊

[@mentarikasih8677]

your tutorial really help me a lot to understand the workflow. If you have experience analyze gwas and also want to make the tutorial, I would appreciate it. Thank you so much ma'am ☺️

[@pauladisanto919]

You are great! Thanks for this amazing tutorial!

[@osmandoluca8347]

@22:00 Instead of doing all that, you can add '-select-genotype "GQ > 10 && DP > 10" \' to the SelectVariants commandline.

[@sujathnair2379]

so are you saying,we can omit all those filters?

[@peipei1770]

Thanks so much for your help this is tremendously helpful! I was wondering where you found the GATK guidelines for the hard filters that you applied? Or if you know them based from experience? I can't seem to find the recommended thresholds anywhere on the GATK website (with the exception of a page that uses QUAL as a filter instead of QD and seems to be outdated). TIA!

[@ramachandran8106]

you are great teacher.. thankyou.

[@venkatakrishnakandalai2571]

Thank you for this very informational video!

[@ОПривет-ъ2ъ]

Awesome tutorial! Thank you so much!

[@rezomgeladze5750]

Great explanation!

[@vardansaroyan7634]

You are amazing. Thanks!!!

[@madhavanjn]

Thanks for ur amazing explanation. Plz keep posting more videos, can u make a video on how to use restapi, github, json, aws etc.

[@RuqaiyaTasneem-z5w]

how to set those filters ? what do all do we have to consider ?

[@OmPrakash-ob5cz]

Any script explanation for diplotype calling?, In the same way as you explained variant calling in a very clear way.

[@alialjizani]

Thank you that was helpful, but what if I have the WES data in form of Excel sheet how can I filter my variants? and is there a tool or a program can do that?

[@sinugeorge9485]

Could you please make a video for GTAK-mutect2 variant calling?

[@shobhitashah1524]

Can you help me with annotation of somatic variants? Are tools for germline and somatic annotation same?

[@farhinnikhat4493]

thanks alot for this amazing video.

[@nikitamaurya4518]

Does this include somatic and germline variant calling workflow?

[@hadieidgah4582]

Fantastic work, thank you and it is always worth to watch your videos till the last second. Can one use this pipeline for WES as well?

[@sgrtools]

This is a great tutorial !. Can you please make a video on "Call somatic mutations using GATK4 Mutect2"?? and a video on "maftools" - R package to analyze somatic .vcf files??" Highly appreciated !

[@Bioinformagician]

I will surely consider covering these topics. Thank you for the suggestion:)

[@Testtesztest12123]

Good job

[@赵彬彬-i8s]

Thanks very much for the video. Could you continue to explain Call somatic mutations with Mutect2?

[@Bioinformagician]

I will surely consider making a video on mutect2

[@gana1263]

​@@Bioinformagicianyes ... requesting a tutorial for somatic variant calling workflow....thank you

[@rajeshsingh-xv7wy]

@Bioinformagician please.....As soon as possible.

[@silvereyes000]

She already got filtered SNPs and Indels. Then why does she again create another file which excluded filtered variants?

[@ayushsafar6289]

thank you very very very much

[@sanjaisrao484]

Mam, please upload the visualization part

[@c.p.8689]

Why don't you just merge indels and snps in one main file and annotate this one main file right away?

[@silvereyes000]

Hi could you please tell how can we filter and annotate in the single file? Actually she separated Indels and SNPs to two separate files. If it's possible to filter and annotate from the results VCF file please give the command as reply

[@wagawsendeku7750]

Thanks for the excellent tutorial👍