User: bigfoot

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bigfoot0
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Posts by bigfoot

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Effect Allele Frequency in base summary statistics for PRSs calculation
... Thanks Sam. So, in the end, only SNPs with EAF in the range 0.01-0.99 should be retained for the analyses.. right? ...
written 18 hours ago by bigfoot0
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Effect Allele Frequency in base summary statistics for PRSs calculation
... I want to use summary statistics containing only the Effect Allele Frequency (EAF) and not the Minor Allele Frequency (MAF) as base dataset for PRS calculation in PRSice2. It would be possible to convert EAF to MAF and then filtering for a MAF threshold of 0.01? Thanks in advance ...
polygenic risk scores gwas prs maf prsice written 4 days ago by bigfoot0 • updated 3 days ago by Sam2.6k
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Effect Allele Frequency (EAF) to Minor Allele Frequency (MAF)
... How could I convert the Effect Allele Frequency (EAF) to Minor Allele Frequency (MAF) in GWAS summary statistics? ...
maf gwas genome-wide genetics genomics written 5 days ago by bigfoot0 • updated 5 days ago by Kevin Blighe54k
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Answer: A: METAL (gwas meta-analysis tool)
... I updated the software, now it works amazingly! ...
written 19 days ago by bigfoot0
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Comment: C: METAL (gwas meta-analysis tool)
... GENOMICCONTROL ON SCHEME SAMPLESIZE OVERLAP ON # trait1 MARKER SNP ALLELE A1 A2 EFFECT log(OR) PVALUE P WEIGHT DONTUSECOLUMN DEFAULTWEIGHT 53293 PROCESS /nfs/home4/polpett/summary_statistics/trait1_eur_jun2017 # trait2 MARKER SNP ALL ...
written 19 days ago by bigfoot0
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METAL (gwas meta-analysis tool)
... Hi everybody I'm using METAL (version released on 2011-03-25) to perform a meta-analysis between several GWASs (genome-wide association studies). The included GWASs contain partly overlapping samples. I'm trying to correct for this source of bias by utilising [the code suggested by the programmers ...
gwas metal meta-analysis genomics bioinformatics written 20 days ago by bigfoot0
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Comment: C: SNP annotation with R and SnpEff
... Did you find a solution? I have to convert 8milion rs# to CHR:position, and I'm looking for a solution. ...
written 8 months ago by bigfoot0
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Comment: C: Search dbSNP for hg19 based coordinates
... Is it sure that the third script will match the exact rs (e.g., rs554008981) and not a similar one (e.g., rs55400898123)? is the option -w useful in that context? (e.g., $ grep -fFw rsIDs.txt hg19.snp151.bed > matches.bed) ...
written 8 months ago by bigfoot0
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Comment: C: Converting SNP from chr:pos to rs number using PLINK?
... Thanks a lot! I have a question. Does "position" in "CHR:POSITION" SNP IDs refer to chromosome start or end position? ...
written 8 months ago by bigfoot0
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PLINK2 and data split by chromosomes
... I have my data in .pgen .bim .fam format split by chromosomes. Could I run all chromosomes at the same time in Plink2 or do I need to merge them in single .pgen .bim .fam files before? ...
genome gwas prs plink snp written 10 months ago by bigfoot0

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