VCF file from DanteLabs Dante Labs does not load in IGV

Question

[urishab]

I have received my VCF SNP file from Dante Labs DanteLabs.com) based on whole genome sequencing. The reference is hg19 When trying to load the VCF file in IGV I receive the following error: Could not create index file: myvcffile.fai

A new file is created with the same name as my VCF file but with extension FAI and with length 0

After that when trying to load the genome again there is no response and nothing is shown.

I have already indexed the VCF file using IGVTools and got the resulting .idx file but this didn't change anything.

Any help?

[urishab]

I should have selected "Load File" and instead selected "Load Genome"

Answer 1

[Pierre Lindenbaum]

could not create index file: myvcffile.fai

i would say you choose a VCF file instead of a FASTA sequence for the reference.

[urishab]

Yes thank you I feel stupid

Answer 2

[Charles Warden]

I would kind of like a chance to critically assess the results from Dante Labs. Plus, I can only personally fund and re-analyze so many products with my own samples.

While I understand everybody may not be as comfortable with data sharing as I am, would you considering sharing at least part of your results?

For example, I have all the data for myself on my PGP page: hu832966

I also have some notes on various companies on this GitHub page: https://github.com/cwarden45/DTC_Scripts

(please note that most comments are actually in subfolders on the GitHub page)

[rob]

Hey! - I've recently purchased WGS from Dante (the 30x product) and plan to upload everything to PGP. When they send the data in (which apparently can take....a while!) I'll happily fire over the FASQ/BAM/VCFs or whatever you need. I'm also awaiting receipt of the 120x test kit as well as their long read product so will eventually have all 3 product datasets that you can analyse (did this so I can partly check their own QC against my own datasets).

If you PM me in a few months time I should have the data

[Charles Warden]

Hi - I probably won't be ordering a Dante Labs kit this year. I'm trying to wrap up the analysis that of what I've submitted so far. Maybe next year :)

I personally probably won't be using your data for analysis, but I think that is helpful. For example, this pre-print discussion indicated one value in having a resource of multiple data types for each person (since the array platform described in that study is different than most DTC companies):

https://www.biorxiv.org/content/10.1101/696799v1#disqus_thread

As of yesterday, there was also a bit of a bug on the PGP site in uploading my Nebula data (the older upload interface worked, but only for small files, like my upgraded V5 23andMe array and my Vitagene genotype data), and your Dante Labs data will be even bigger. Nevertheless, if you are curious, I do have my notes (mostly in subfolders) on GitHub, although I apologize in advance for the information overload (I will convert some main points to a blog post, but I think I have a few more things to work on first):

https://github.com/cwarden45/DTC_Scripts

https://github.com/cwarden45/Bastu_Cat_Genome

(I realize one link is the same, but it has been updated). For example, I believe these sections are new:

https://github.com/cwarden45/DTC_Scripts/tree/master/Nebula

https://github.com/cwarden45/DTC_Scripts/tree/master/Color

https://github.com/cwarden45/DTC_Scripts/tree/master/Nutrigenomics

https://github.com/cwarden45/DTC_Scripts/tree/master/FamilyTreeDNA

https://github.com/cwarden45/DTC_Scripts/tree/master/Genes_for_Good/RFMix_ReAnalysis/Downsample_Test