User: landscape95

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landscape95160
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Posts by landscape95

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Comment: C: Get SNP information with association test with PLINK
... Thank you so much, Chang. ...
written 1 day ago by landscape95160
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Comment: C: Get SNP information with association test with PLINK
... Thanks for your prompt reply, Here is the code and output of plink1.9: plink --bfile test --assoc --adjust --out output --allow-no-sex --threads 100 PLINK v1.90b4.1 64-bit (30 Mar 2017) Options in effect: --adjust --allow-no-sex --assoc --bfile test --out ...
written 1 day ago by landscape95160
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MTG2 error forrtl: severe (174): SIGSEGV, segmentation fault occurred
... I am calculating the mean and variance between discovery and target samples using MTG2. After I made a binary grm from plink, I used MTG2 for calculation. Has anyone experienced this problem with MTG2 before? I made sure the the id of the discovery and target samples order is the same as the grm id ...
mtg2 written 2 days ago by landscape95160
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Get SNP information with association test with PLINK
... Hi everyone, Does anyone know how to get the SNP information containing CHR ID A1 REF etc with association test on quantitative trait from plink (output file: .qassoc). I done the association test and I want to obtain these information also. In --linear with plink2, I have it, but with plink1.9 ass ...
gwas plink written 3 days ago by landscape95160 • updated 2 days ago by zx87546.5k
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Comment: C: Plink2 error: Skipping --glm regression on phenotype 'PHENO1' since variance inf
... Hi Chang, It seems like my unique values of centre data is less than the batch data. But I have no problem with batch but problem with centre, I still don't have any clue why it says Variance inflation factor is too high for to centre. Is there anyway to figure out it by hand/debug manually? Thank ...
written 17 days ago by landscape95160
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PRSice threshold result is not as expected
... Hi everyone, I am doing the PRS with [PRSice](https://choishingwan.github.io/PRSice/), I set as follow ... --lower 0 \ --interval 0.01 \ --upper 0.85 \ ... the result in the *.prsice* is as follow Set Threshold R2 P Coefficient Standard.Error Num_SNP Base 0.11 0.05 ...
prsice gwas written 21 days ago by landscape95160 • updated 10 days ago by zx87546.5k
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Comment: C: Plink2 error: Skipping --glm regression on phenotype 'PHENO1' since variance inf
... Hi Chang, I've done what you said but it says, may I need your support? Thank you very much! Here is my code: /home/joe/Tools/plink2/plink2 --bfile ukbb_dis_relationship --pheno Covariate_rel.tsv --pheno-name height --covar Covariate_rel.tsv --covar-name yob, sex, age --input-missing-phenotype ...
written 25 days ago by landscape95160
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Using SSrGE for SNV calling
... Hi everyone, I came across the paper of of Olivier et. al. https://www.nature.com/articles/s41467-018-07170-5 and here I apply the package SSrGE for SNV calling https://github.com/lanagarmire/SSrGE. I used GATK3 for SNV calling. Here is my code for debugging: /usr/lib/jvm/java-8-oracle/jre/bin/ ...
ssrge snv written 26 days ago by landscape95160
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Comment: C: Viewing large compressed genetic relationship matrix .grm file
... Thank you! I want to do some samples clustering based on the relationship between individuals. ...
written 29 days ago by landscape95160
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Viewing large compressed genetic relationship matrix .grm file
... Hi everyone, I now have a large compressed genetic relationship matrix (.grm.gz) file around 870 GB. As I know, this file is the edge list of individuals via their relationship. Now I want to get this information of relationship between individual i and j but the compressed file is already large, ca ...
gcta written 29 days ago by landscape95160

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