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Mithras Enkidu
02-14-2021, 12:01 PM
Hi!

I need your help!
I recently took a test with Dante Labs. This company proposes to download their files in ten different formats. I sent them Davidski to have my Global 25 done from that company but he says they're too big. Does someone know which exact file format I have to send him?

Thank you very much!

maroco
02-14-2021, 12:10 PM
Have you converted your file through wgs studio first?

ssamlal
02-14-2021, 10:11 PM
Hi!

I need your help!
I recently took a test with Dante Labs. This company proposes to download their files in ten different formats. I sent them Davidski to have my Global 25 done from that company but he says they're too big. Does someone know which exact file format I have to send him?

Thank you very much!

See https://wgsextract.github.io/ for the WGS Extract program and manual.

Use WGS Extract and your Dante Labs 30x WGS BAM and BAM.bai files to create one or more autosomal file(s). I chose the "combined file - RECOMMENDED" option. The steps are in the manual.

Upload the zip file to a shared drive (e.g. Google Drive), and provide Davidski with the link to the shared file.

Mithras Enkidu
02-16-2021, 04:52 PM
Hi! Thank you very much!

However when I'm trying it, I'm receiving the following message:
"The BAM file and the path of the BAM file must not contain spaces or special chars. Please rename the path or the BAM file to meet these criteria."
How can I do it? Thanks! ^^

jadegreg
02-17-2021, 02:04 PM
I think the .bam file should be in the same folder as WGS Extract, or actually in the WGS extract folder

ssamlal
02-17-2021, 07:59 PM
Check the path where your BAM & BAI files are stored. Make sure there are no spaces between words (I replaced spaces with underscores). Also make sure you don't have special characters (the "&" symbol is one that shows up the most; remove it or replace it with the word "and").

Also check the date and time of your bai file. It should be after the date/time of your BAM file. I downloaded the bai file first, then had to delete and download it again. Make sure both files are in the same folder.

43382
43372

ssamlal
02-17-2021, 08:03 PM
ignore; I was able to add the screenshot to my previous post.

Mithras Enkidu
02-22-2021, 11:43 PM
Thank you very much! I'm going to try it! :)

Mithras Enkidu
02-23-2021, 01:40 AM
Hi! The name of the file is "GFX0435462", with absolutely no space beween the letters and numbers and no date attached with the tittle either! I changed this name into into "AND", I trid it again, but I still get that same damn error message!
Do you please know another software? I'm difinitely done with this useless WSGExtract program!
Thank you!

ssamlal
02-23-2021, 08:25 PM
Hey Mithras,

Did you look at the screenshot in my previous post?

Check the path where you file is stored (using Windows file explorer).

My path was this (notice the spaces in the folder names):
D\DNA Data Files\Dante Labs\GFX0450466

I updated all the folder names in the path (replacing spaces with underscores):
D\DNA_Data_Files\Dante_Labs\GFX0450466

You should see the file date in Windows file explorer.

43477

Mithras Enkidu
02-24-2021, 06:05 PM
Wow! Thank you so much! (Well, no, I couldn't open your previous screenshot. However I could watch this one.)
The software has run! Nevertheless it says it doesn't find the BAM.BAI file (wich is there too). It also shows the following window: "This BAM file has a very low average reading depth. This can lead to incorrect data. If you have a bam file from a better sequencing run for this person, then you should better use that one."
What can I do?
Thanks a lot!

Mithras Enkidu
02-24-2021, 06:43 PM
Wow! Thank you so much! (Well, no, I couldn't open your previous screenshot. However I could watch this one.)
The software has run! Nevertheless it says it doesn't find the BAM.BAI file (wich is there too). It also shows the following window: "This BAM file has a very low average reading depth. This can lead to incorrect data. If you have a bam file from a better sequencing run for this person, then you should better use that one."
What can I do?
Thanks a lot!

P.S. = Do I have to merge my BAM and my BAM.BAI files? If yes, how can I do it?
Thanks.

Mithras Enkidu
02-25-2021, 12:53 AM
Wow! Thank you so much! (Well, no, I couldn't open your previous screenshot. However I could watch this one.)
The software has run! Nevertheless it says it doesn't find the BAM.BAI file (wich is there too). It also shows the following window: "This BAM file has a very low average reading depth. This can lead to incorrect data. If you have a bam file from a better sequencing run for this person, then you should better use that one."
What can I do?
Thanks a lot!

P.S. = Do I have to merge my BAM and my BAM.BAI files? If yes, how can I do it?
Thanks.

ssamlal
02-26-2021, 04:52 PM
Wow! Thank you so much! (Well, no, I couldn't open your previous screenshot. However I could watch this one.)
The software has run! Nevertheless it says it doesn't find the BAM.BAI file (wich is there too). It also shows the following window: "This BAM file has a very low average reading depth. This can lead to incorrect data. If you have a bam file from a better sequencing run for this person, then you should better use that one."
What can I do?
Thanks a lot!

P.S. = Do I have to merge my BAM and my BAM.BAI files? If yes, how can I do it?
Thanks.

You don't have to merge the BAM and bai files.

In a previous post I mentioned that you should check the date and time of your bai file. It should be after the date/time of your BAM file (refer to the screenshot in my last post). If it's before then delete and download it again.

I haven't seen the "low coverage" error myself and the online manual only mentions this error if a FTDNA BAM file is selected.

Are you able to post screenshots of the "Settings" tab and also after clicking the "Show statistics..." button on the "Other" tab?

It's possible that there is an issue with the quality your BAM file, in which case you should reach out to Dante Labs.

Mithras Enkidu
02-26-2021, 07:07 PM
OK, thanks. First of all, I delete and re-download my files, in the case a problem occured during my first download (?).
I'll let you know.

Once again, thank you very much for your precious help!

Mithras Enkidu
02-26-2021, 11:20 PM
Hi back! I was right to download the file again, as it seems that it was corrupted! Here is what I get now:

43565435664356743568

Mithras Enkidu
03-02-2021, 11:02 AM
OK, I give it up!
I'm unable to use WSGExtract. Now it doesn't find the /tmp file.
I'm really fed up with it.

However Dante Labs also provides a VCF (TAR.GZ file). I wish I could convert it with DNA Kit Studio, but I really don't understand why this software aks me a Raw Data Output!
What is it supposed to be?
Thanks!

EDIT: It is not explained in the Support section!

Mithras Enkidu
03-02-2021, 11:02 AM
Here is the screenshot.
43634

altvred
03-02-2021, 11:14 AM
Here is the screenshot.
43634
You can use PLINK (https://www.cog-genomics.org/plink/1.9/data#recode) to convert a VCF file to a 23andMe format. Not too complicated of a procedure but I would advise you to take a few minutes and read the page I linked on how to use the program.

Mithras Enkidu
03-18-2021, 02:24 AM
Hi! Thank you very much for yor help!

I wasn't abble to use WGSExtract as I really suck in informatics. It's really not my thing!
However I finally have been able to convert my SNP.VCF file to a 23andMe file thanks to DNA Kit Studio! :D
Honestly, I needed to try a lots of times before getting it!
But I finally could get my G25 from my Dante Labs data!
It has been a long, long story!

lacreme
03-18-2021, 08:27 AM
Hi! Thank you very much for yor help!

I wasn't abble to use WGSExtract as I really suck in informatics. It's really not my thing!
However I finally have been able to convert my SNP.VCF file to a 23andMe file thanks to DNA Kit Studio! :D
Honestly, I needed to try a lots of times before getting it!
But I finally could get my G25 from my Dante Labs data!
It has been a long, long story!

What did you end up sending to get your G25 coordinates ? The combined file or the conversion to one of the various companies formats ? I mean from the WGSextract output

dosas
03-18-2021, 08:40 AM
What did you end up sending to get your G25 coordinates ? The combined file or the conversion to one of the various companies formats ? I mean from the WGSextract output

The 23ame v3 gives the lowest distances, even compared to the ALL_SNPS one.

lacreme
03-18-2021, 09:23 AM
The 23ame v3 gives the lowest distances, even compared to the ALL_SNPS one.

Thanks! I'll tell my friend to send that then. Do you know if David can create phased G25 coordinates for an untested parent too ?

dosas
03-18-2021, 02:29 PM
Thanks! I'll tell my friend to send that then. Do you know if David can create phased G25 coordinates for an untested parent too ?

You can use the option on Genoplot for ghosted data.

lacreme
03-18-2021, 03:37 PM
You can use the option on Genoplot for ghosted data.

Can't get it to work, tried uploading his mother's data but it's not showing on the dropdown list when I'm trying to choose the parent to substract (or on any G25 function really )

dosas
03-18-2021, 03:42 PM
Can't get it to work, tried uploading his mother's data but it's not showing on the dropdown list when I'm trying to choose the parent to substract (or on any G25 function really )

It works, I've used it numerous times.

You choose subtract and then subtract the parent/grandparent/w,e generation from the base child/grandchild/w.e. The produced data is the other 50% that is ghosted. You can even subtract %s.

lacreme
03-18-2021, 04:59 PM
It works, I've used it numerous times.

You choose subtract and then subtract the parent/grandparent/w,e generation from the base child/grandchild/w.e. The produced data is the other 50% that is ghosted. You can even subtract %s.

Unfortunately I have tried uploading her data many times and I can never find her on the list of available profiles/users/samples . Tried setting her data availability both public and private but with no luck