Question about converting converting result.mat to csv file and redefine genetic loci based on FUMA

[zqsha]

Hi experts,
Thanks for developing such an amazing toolbox. I try to run the condFDR and conjFDR with the example data. It worked very well. But, when I convert result.mat to csv file and redefine genetic loci based on FUMA, I met a bug. Could you help me to take a look at it? Now, I have result.mat, and then
Step 1, I used the following command line to covert the result.mat to result.mat.csv file
Python fdrmat2csv.py
--mat result.mat
--ref 9545389.ref
--out result.mat.csv
In this step, I got the result.mat.csv, without any bugs. When I check the data within result.mat.csv, there are 9545380 SNPs, in which 5997733 SNPs have FDR values. That means pleioFDR only estimates condFDR/conjFDR across these 5997733 SNPs.

Step 2, I used the following command line to clump the data and generate the significant loci based on FUMA logic
Python sumstats.py clump
--clump-field FDR
--force
--plink /software/plink_1.9/plink
--bfile-chr /pleiofdr/ref9545380_bfile/chr@
--exclude-ranges ['6:25119106-33854733', '8:7200000-12500000']
--clump-p1 0.05
--out result.clump

In the command line,
“--clump-field” specifies the column used for clumping.
“--plink” specifies the link to plink toolbox. Here, I tried plink 1.07, plink 1.9 and plink 2.0.
“--bfile-chr” specifies the reference bfile, which can be downloaded by “wget https://precimed.s3-eu-west-1.amazonaws.com/pleiofdr/ref9545380_bfile.tar.gz”
“--exclude-ranges” indicates the regions that we need to exclude when defining the significant genomic loci
“--clump-p1” specifies the significance threshold for index SNPs. So, condFDR analysis would set 0.01, while conjFDR analysis would set 0.05. Please correct me, if I did not describe them correctly.

When I run Step 2, it reported the following error,

It seems the toolbox did not recognize the format of excluded regions that I set. Do you have any thoughts on fixing it issue? Any suggestions were appreciated. Thank you so much in advance.

[zainab-cpu]

hello dear! Have you found the solution? if Yes, kindly let us know

[baiqiang963]

Python sumstats.py clump
--clump-field FDR
--force
--plink /software/plink_1.9/plink
--bfile-chr /pleiofdr/ref9545380_bfile/chr@
--exclude-ranges ['6:25119106-33854733', '8:7200000-12500000']
--clump-p1 0.05
--out result.clump

dont use '[]' and ',' in ''--exclude-ranges"

just try:
Python sumstats.py clump
--clump-field FDR
--force
--plink /software/plink_1.9/plink
--bfile-chr /pleiofdr/ref9545380_bfile/chr@
--exclude-ranges '6:25119106-33854733' '8:7200000-12500000'
--clump-p1 0.05
--out result.clump

[zainab-cpu]

Python sumstats.py clump --clump-field FDR --force --plink /software/plink_1.9/plink --bfile-chr /pleiofdr/ref9545380_bfile/chr@ --exclude-ranges ['6:25119106-33854733', '8:7200000-12500000'] --clump-p1 0.05 --out result.clump

dont use '[]' and ',' in ''--exclude-ranges"

just try: Python sumstats.py clump --clump-field FDR --force --plink /software/plink_1.9/plink --bfile-chr /pleiofdr/ref9545380_bfile/chr@ --exclude-ranges '6:25119106-33854733' '8:7200000-12500000' --clump-p1 0.05 --out result.clump

Hello there! I followed your instructions precisely, but unfortunately, I detected no significant SNPs in my files. I also couldn't identify any significant SNPs based on the provided example in this software. Any thoughts?

[baiqiang963]

You should unzip your ‘/path/pleiofdr-master/ref9545380_bfile.tar.gz’ into a new folder named ‘ref9545380’. Then, you can change'--bfile-chr /pleiofdr/ref9545380_bfile/chr@' into ' path/ref9545380/chr'.

[zainab-cpu]

You should unzip your ‘/path/pleiofdr-master/ref9545380_bfile.tar.gz’ into a new folder named ‘ref9545380’. Then, you can change'--bfile-chr /pleiofdr/ref9545380_bfile/chr@' into ' path/ref9545380/chr'.

thank you for your response. But I was doing the same and still got the error after running the script. Error (no variants pass significant threshold. WARNING: No clumped files found - could it be that no variants pass significant threshold?)

[Licun1]

@zainab-cpu Have you fixed this issue? If yes, could you tell us the solution?

[Zhangzzzzzy]

Have you solved the problem, please?