Nebula k36 vs Gedmatch

[Genetics189291]

Why is my nebula different from my .txt file on Gedmatch. I used wgs extract for my cram file to create a 23andme txt file so I’m little confused why they are different

[Capsian20]

maybe there difference data ?

[miquirumba]

Surely Nebula used different SNP collection as AADR or Human Origins

[Genetics189291]

Surely Nebula used different SNP collection as AADR or Human Origins

Not sure but it a a big difference from the file I created, it would be good to know so I can create an autosomal file with similar result a

[miquirumba]

Surely Nebula used different SNP collection as AADR or Human Origins

Not sure but it a a big difference from the file I created, it would be good to know so I can create an autosomal file with similar result a

I checked last WGSEXTRACT Dev updated a few days ago trying to do an AADR kit with my BAM but it didn't work. It's only the button 
You could run bcftools mpileup with AADR sites template in bed or tab format (as target file)

[Genetics189291]

Surely Nebula used different SNP collection as AADR or Human Origins

Not sure but it a a big difference from the file I created, it would be good to know so I can create an autosomal file with similar result a

I checked last WGSEXTRACT Dev updated a few days ago trying to do an AADR kit with my BAM but it didn't work. It's only the button 
You could run bcftools mpileup with AADR sites template in bed or tab format (as target file)

Which one did you download because I couldn’t see it. I might do that do you have a link to Aadr in that format

[miquirumba]

Not sure but it a a big difference from the file I created, it would be good to know so I can create an autosomal file with similar result a

I checked last WGSEXTRACT Dev updated a few days ago trying to do an AADR kit with my BAM but it didn't work. It's only the button 
You could run bcftools mpileup with AADR sites template in bed or tab format (as target file)

Which one did you download because I couldn’t see it. I might do that do you have a link to Aadr in that format

I have a DIY template for 1240K in my usegalaxy account 

https://usegalaxy.org/api/datasets/f9cad...to_ext=bed
I haven't check yet AADR template from Reich Lab, Harvard 
however, it's easy to make one if you have a AADR VCF or BED with bcftools query selecting only the colums you need for a template (chr, pos)

[Genetics189291]

I checked last WGSEXTRACT Dev updated a few days ago trying to do an AADR kit with my BAM but it didn't work. It's only the button 
You could run bcftools mpileup with AADR sites template in bed or tab format (as target file)

Which one did you download because I couldn’t see it. I might do that do you have a link to Aadr in that format

I have a DIY template for 1240K in my usegalaxy account 

https://usegalaxy.org/api/datasets/f9cad...to_ext=bed
I haven't check yet AADR template from Reich Lab, Harvard 
however, it's easy to make one if you have a AADR VCF or BED with bcftools query selecting only the colums you need for a template (chr, pos)

Is it possible to use my cram to create this or my current autosomal file i produced

[miquirumba]

Which one did you download because I couldn’t see it. I might do that do you have a link to Aadr in that format

I have a DIY template for 1240K in my usegalaxy account 

https://usegalaxy.org/api/datasets/f9cad...to_ext=bed
I haven't check yet AADR template from Reich Lab, Harvard 
however, it's easy to make one if you have a AADR VCF or BED with bcftools query selecting only the colums you need for a template (chr, pos)

Is it possible to use my cram to create this or my current autosomal file i produced

I just read in last AADR paper
https://www.nature.com/articles/s41597-024-03031-7
they combined samples 1240K with Affinometrix 640,000 SNPs therefore we need a combined template bed or tab file with all chrom, pos in B37/hg19  reference 
You can use 1240k template I shared by link to make a VCF from your CRAM with bcftools mpileup (as target file) the call only these SNPs with bcftools call. it's easy convert this VCF to 23andme format with PLINK
The main AADR samples are formatted with 1240K positions

sorry if you CRAM is Nebula alignment against hg38 this template doesn't work. you need a liftover tool to convert b37 positions to hg38

[Genetics189291]

I have a DIY template for 1240K in my usegalaxy account 

https://usegalaxy.org/api/datasets/f9cad...to_ext=bed
I haven't check yet AADR template from Reich Lab, Harvard 
however, it's easy to make one if you have a AADR VCF or BED with bcftools query selecting only the colums you need for a template (chr, pos)

Is it possible to use my cram to create this or my current autosomal file i produced

I just read in last AADR paper
https://www.nature.com/articles/s41597-024-03031-7
they combined samples 1240K with Affinometrix 640,000 SNPs therefore we need a combined template bed or tab file with all chrom, pos in B37/hg19  reference 
You can use 1240k template I shared by link to make a VCF from your CRAM with bcftools mpileup (as target file) the call only these SNPs with bcftools call. it's easy convert this VCF to 23andme format with PLINK
The main AADR samples are formatted with 1240K positions

sorry if you CRAM is Nebula alignment against hg38 this template doesn't work. you need a liftover tool to convert b37 positions to hg38

Can’t I do this with wgs extract how would I input it into wgs extract

[miquirumba]

Is it possible to use my cram to create this or my current autosomal file i produced

I just read in last AADR paper
https://www.nature.com/articles/s41597-024-03031-7
they combined samples 1240K with Affinometrix 640,000 SNPs therefore we need a combined template bed or tab file with all chrom, pos in B37/hg19  reference 
You can use 1240k template I shared by link to make a VCF from your CRAM with bcftools mpileup (as target file) the call only these SNPs with bcftools call. it's easy convert this VCF to 23andme format with PLINK
The main AADR samples are formatted with 1240K positions

sorry if you CRAM is Nebula alignment against hg38 this template doesn't work. you need a liftover tool to convert b37 positions to hg38

Can’t I do this with wgs extract how would I input it into wgs extract

I was talking about that with Randy Harr (WGSExtract programmer) a few months ago. he suggested I used 23andmeAPI header after copying 1240K.tab.gz template into  WGSE microarrays  folder. There must be a few code lines to program 1240K microarray extraction although I still haven't find a script running fine in WGSE for 1240K or AADR

[Genetics189291]

I just read in last AADR paper
https://www.nature.com/articles/s41597-024-03031-7
they combined samples 1240K with Affinometrix 640,000 SNPs therefore we need a combined template bed or tab file with all chrom, pos in B37/hg19  reference 
You can use 1240k template I shared by link to make a VCF from your CRAM with bcftools mpileup (as target file) the call only these SNPs with bcftools call. it's easy convert this VCF to 23andme format with PLINK
The main AADR samples are formatted with 1240K positions

sorry if you CRAM is Nebula alignment against hg38 this template doesn't work. you need a liftover tool to convert b37 positions to hg38

Can’t I do this with wgs extract how would I input it into wgs extract

I was talking about that with Randy Harr (WGSExtract programmer) a few months ago. he suggested I used 23andmeAPI header after copying 1240K.tab.gz template into  WGSE microarrays  folder. There must be a few code lines to program 1240K microarray extraction although I still haven't find a script running fine in WGSE for 1240K or AADR

Does he have plans to add it in the future?

[miquirumba]

Can’t I do this with wgs extract how would I input it into wgs extract

I was talking about that with Randy Harr (WGSExtract programmer) a few months ago. he suggested I used 23andmeAPI header after copying 1240K.tab.gz template into  WGSE microarrays  folder. There must be a few code lines to program 1240K microarray extraction although I still haven't find a script running fine in WGSE for 1240K or AADR

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

[Genetics189291]

I was talking about that with Randy Harr (WGSExtract programmer) a few months ago. he suggested I used 23andmeAPI header after copying 1240K.tab.gz template into  WGSE microarrays  folder. There must be a few code lines to program 1240K microarray extraction although I still haven't find a script running fine in WGSE for 1240K or AADR

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

I have the latest and can’t see the option I don’t agree with combining them all though but would be nice to have as an option

[Genetics189291]

I was talking about that with Randy Harr (WGSExtract programmer) a few months ago. he suggested I used 23andmeAPI header after copying 1240K.tab.gz template into  WGSE microarrays  folder. There must be a few code lines to program 1240K microarray extraction although I still haven't find a script running fine in WGSE for 1240K or AADR

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