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JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
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MTAG results do not include some Chromosomes #130

Open osoremekun opened 3 years ago

osoremekun commented 3 years ago

Hi, I was wondering what could be the problem. My MTAG results do not include chromosomes beyond a particular chromosome number. I have SNPs up to chromosome 11, but beyond this, no SNPs are found.

paturley commented 3 years ago

Can you share the log file? it's difficult to diagnose the problem without additional information.

On Mon, Apr 19, 2021 at 4:35 PM OPS001 @.***> wrote:

Hi, I was wondering what could be the problem. My MTAG results do not include chromosomes beyond a particular chromosome number. I have SNPs up to chromosome 11, but beyond this, no SNPs are found.

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osoremekun commented 3 years ago

Attached is the log file. A1_A2_Meta_results.log

paturley commented 3 years ago

Looking at this log file, it looks like your results should have roughly 3 million SNPs. Is that right? And all 3 million are on chromosomes 1-11?

On Tue, Apr 20, 2021 at 1:47 AM OPS001 @.***> wrote:

Attached is the log file. A1_A2_Meta_results.log https://github.com/JonJala/mtag/files/6340926/A1_A2_Meta_results.log

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osoremekun commented 3 years ago

Yes, you are right.

paturley commented 3 years ago

It looks like all the SNPs are being dropped in the merge step of the analysis. Can you confirm that there are SNPs on chromosomes >11 that should be matched and aren't?

On Wed, Apr 21, 2021 at 2:45 AM OPS001 @.***> wrote:

Yes, you are right.

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osoremekun commented 3 years ago

There are quite a number of SNPs beyond chromosome 11 that are supposed to be merged that are not merged.

paturley commented 3 years ago

Can you identify a single SNP on chromosome 12 that is present in both data sets and which satisfies MTAG's filters and paste the row of the GWAS file corresponding to that SNP in each file? That might help identify what is going on.

On Wed, Apr 21, 2021 at 8:51 AM OPS001 @.***> wrote:

There are quite a number of SNPs beyond chromosome 11 that are supposed to be merged that are not merged.

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