W8: Variant Calling with GATK - Day 1

This workshop uses materials developed by the Broad Institute to teach Variant Calling with GATK. Attendees with no prior experience in variant calling are recommended to review all of the materials below before coming to the workshop. This early preparation will allow a focus on the specific issues of running GATK on the UCLA hoffman2 cluster rather than introducing the GATK variant calling pipeline. There will also be a focus on post variant discovery quality control steps as time allows.
Course Materials - drive.google.com/drive/folder...

[@sfmambero]

11:00 lecture begins
25:50 VCF files
53:50 GATK workflow

[@satheatul1]

Thank you very much for showing how to use GATK for variant calling. You made variant calling look easy even for beginners like me. Please keep uploading such hands on training workshops.

[@jsha129]

Nice explanation. covers a lot of basic grounds. Thanks!

[@lionamaya3514]

This is just great lecture! Thank you so much!!

[@xiaolongma9806]

0 | 0 indicates phased, which means I can tell which allele came from which parent, and 0/0 indicates unphased. I just clarify this information here in case you feel confused about the phasing

[@akimomo8463]

thank you for this workshop, got a lot of help from it

[@berenicebajoleyva439]

Link to the resources from the Broad Institute:
console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/

[@ashleywang2748]

Thanks for the nice lecture, could you also post the link of the materials, please?

[@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

[@shobhitashah1524]

Very nice lecture. Thank you. I want to Learn different NGS pipelines, beginning with DNAseq , RNAseq, Chipseq, CRISPER. One by one. Can you suggest me different courses or project?

[@shobhitashah1524]

Can you suggest me where can I get the VCF file for case and control?

[@shristibiswas3875]

I have a few doubts regarding the VCF file, I need explanations on where should I post them for quick solutions.

[@briansalkas349]

Is there any place I can go to get these files? I was looking all over and in the end I got an error about non-overlapping contigs because my reference genome did not come from the same source as my bam files.

[@briansalkas349]

I finally got it to work, I had to unzip the indel and snp files and use sed to remove the chr in the names. Doing this is not ideal but it worked for this practice so it's good enough for me.

[@Hotarunohikatte]

Tomato is a fruit

[@alexanderyesaya3178]

How can I book a session with you?

[@ifyifemanima3972]

I did not find this helpful at all.