Nebula k36 vs Gedmatch

[miquirumba]

Does he have plans to add it in the future?

He has updated WGSE DEV a few weeks ago. He said that maybe it would be better to combine all SNPs (AADR, 1240K, HO and others) in the same template as allCombined.kit that's easier to program because all new sci raw data templates are subset of main combined tab.gz

Do you have the link for the aadr 1240k tab.gz file

same format as All_SNPs_GRCh37_ref.tab

https://drive.google.com/file/d/1tzHqeKV...sp=sharing

I had problems to index with tabix, you could unzip and combine with All_SNPs_GRCh37_ref.tab to get all SNPs (maybe will work saved as All_SNPs_GRCh37_ref.tab)
I haven't time now to work in WGSE development, perhaps next month

[Genetics189291]

He has updated WGSE DEV a few weeks ago. He said that maybe it would be better to combine all SNPs (AADR, 1240K, HO and others) in the same template as allCombined.kit that's easier to program because all new sci raw data templates are subset of main combined tab.gz

Do you have the link for the aadr 1240k tab.gz file

same format as All_SNPs_GRCh37_ref.tab

https://drive.google.com/file/d/1tzHqeKV...sp=sharing

I had problems to index with tabix, you could unzip and combine with All_SNPs_GRCh37_ref.tab to get all SNPs (maybe will work saved as All_SNPs_GRCh37_ref.tab)
I haven't time now to work in WGSE development, perhaps next month

Let me try this I’ll get back to you

[Genetics189291]

He has updated WGSE DEV a few weeks ago. He said that maybe it would be better to combine all SNPs (AADR, 1240K, HO and others) in the same template as allCombined.kit that's easier to program because all new sci raw data templates are subset of main combined tab.gz

Do you have the link for the aadr 1240k tab.gz file

same format as All_SNPs_GRCh37_ref.tab

https://drive.google.com/file/d/1tzHqeKV...sp=sharing

I had problems to index with tabix, you could unzip and combine with All_SNPs_GRCh37_ref.tab to get all SNPs (maybe will work saved as All_SNPs_GRCh37_ref.tab)
I haven't time now to work in WGSE development, perhaps next month

I combined and then sorted by chromosome position if you want the file I can give it to you.

[miquirumba]

Do you have the link for the aadr 1240k tab.gz file

same format as All_SNPs_GRCh37_ref.tab

https://drive.google.com/file/d/1tzHqeKV...sp=sharing

I had problems to index with tabix, you could unzip and combine with All_SNPs_GRCh37_ref.tab to get all SNPs (maybe will work saved as All_SNPs_GRCh37_ref.tab)
I haven't time now to work in WGSE development, perhaps next month

I combined and then sorted by chromosome position if you want the file I can give it to you.

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version

[Genetics189291]

same format as All_SNPs_GRCh37_ref.tab

https://drive.google.com/file/d/1tzHqeKV...sp=sharing

I had problems to index with tabix, you could unzip and combine with All_SNPs_GRCh37_ref.tab to get all SNPs (maybe will work saved as All_SNPs_GRCh37_ref.tab)
I haven't time now to work in WGSE development, perhaps next month

I combined and then sorted by chromosome position if you want the file I can give it to you.

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version

I’ll do it when I get home from work

[Genetics189291]

same format as All_SNPs_GRCh37_ref.tab

https://drive.google.com/file/d/1tzHqeKV...sp=sharing

I had problems to index with tabix, you could unzip and combine with All_SNPs_GRCh37_ref.tab to get all SNPs (maybe will work saved as All_SNPs_GRCh37_ref.tab)
I haven't time now to work in WGSE development, perhaps next month

I combined and then sorted by chromosome position if you want the file I can give it to you.

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version

e

easyupload.io/wug627

That’s the download link let me know how it goes

[miquirumba]

I combined and then sorted by chromosome position if you want the file I can give it to you.

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version
[/quo

[quote pid="36573" dateline="1728841807"]
e

easyupload.io/wug627

That’s the download link let me know how it goes

FILE NOT FOUND
File may be expired or removed by easyupload.io because of a policy violation

[Genetics189291]

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version
[/quo

[quote pid="36573" dateline="1728841807"]
e

easyupload.io/wug627

That’s the download link let me know how it goes

FILE NOT FOUND
File may be expired or removed by easyupload.io because of a policy violation

[/quote]
Let me reupload it somewhere else

[Genetics189291]

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version
[/quo

[quote pid="36573" dateline="1728841807"]
e

easyupload.io/wug627

That’s the download link let me know how it goes

FILE NOT FOUND
File may be expired or removed by easyupload.io because of a policy violation

[/quote]
It’s still showing for me weird I’ll upload it else where though

[Genetics189291]

share the link to your combined tab file, please
I'll try to run in WGSE DEV Ubuntu version
[/quo

[quote pid="36573" dateline="1728841807"]
e

easyupload.io/wug627

That’s the download link let me know how it goes

FILE NOT FOUND
File may be expired or removed by easyupload.io because of a policy violation

[/quote]
https://gofile.io/d/d2egCn

here is a new link

[miquirumba]

[quote pid="36573" dateline="1728841807"]
e

easyupload.io/wug627

That’s the download link let me know how it goes

FILE NOT FOUND
File may be expired or removed by easyupload.io because of a policy violation

https://gofile.io/d/d2egCn

here is a new link
[/quote]
downloaded, thanks

3,314,072 SNPs with rsID, a good improvement. I'll check this week

[miquirumba]

most of new SNPs are duplicates, only about 200,000 new SNPs running bcftools
0 number of records: 2495890
SN 0 number of no-ALTs: 1775780
SN 0 number of SNPs: 718483
SN 0 number of MNPs: 0
SN 0 number of indels: 1627

surely is the reason WGSE crashed trying to extract them
I'll remove duplicates this week and add Twist Bioscience 1.4M 100,000 extra SNPs

[Genetics189291]

most of new SNPs are duplicates, only about 200,000 new SNPs running bcftools
0 number of records: 2495890
SN 0 number of no-ALTs: 1775780
SN 0 number of SNPs: 718483
SN 0 number of MNPs: 0
SN 0 number of indels: 1627

surely is the reason WGSE crashed trying to extract them
I'll remove duplicates this week and add Twist Bioscience 1.4M 100,000 extra SNPs

What I tried to do is take the dnakitstudio template 1240k and replace it in the wgsextractfolder which worked but only issue is it caused too much no calls

[miquirumba]

most of new SNPs are duplicates, only about 200,000 new SNPs running bcftools
0 number of records: 2495890
SN 0 number of no-ALTs: 1775780
SN 0 number of SNPs: 718483
SN 0 number of MNPs: 0
SN 0 number of indels: 1627

surely is the reason WGSE crashed trying to extract them
I'll remove duplicates this week and add Twist Bioscience 1.4M 100,000 extra SNPs

What I tried to do is take the dnakitstudio template 1240k and replace it in the wgsextractfolder which worked but only issue is it caused too much no calls

There is no reason for a lot no calls, I am sure you are using dnakutStudio Build37 template running against your hg38 CRAM. Different reference genomes don't match many SNPs then you have a lot of no calls because you need a 1240k for hg38 reference

[Genetics189291]

most of new SNPs are duplicates, only about 200,000 new SNPs running bcftools
0 number of records: 2495890
SN 0 number of no-ALTs: 1775780
SN 0 number of SNPs: 718483
SN 0 number of MNPs: 0
SN 0 number of indels: 1627

surely is the reason WGSE crashed trying to extract them
I'll remove duplicates this week and add Twist Bioscience 1.4M 100,000 extra SNPs

What I tried to do is take the dnakitstudio template 1240k and replace it in the wgsextractfolder which worked but only issue is it caused too much no calls

There is no reason for a lot no calls, I am sure you are using dnakutStudio Build37 template running against your hg38 CRAM. Different reference genomes don't match many SNPs then you have a lot of no calls because you need a 1240k for hg38 reference

It’s still using a lift over, all the templates are hg37 it just lift overs my cram
When converting the file. Do you have a template for hg38?