User: bigfoot

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bigfoot0
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Posts by bigfoot

<prev • 13 results • page 1 of 2 • next >
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Removing NaN values from GWAS summary statistics?
... Dear all, How can I be sure that I have also removed all the missing values from the GWAS summary statistics? I have already applied some general Quality Controls steps (in the script below, names are in place of the number of the columns): cat file_input_sumstats | \ awk 'NR==1 || ($MAF &g ...
gwas unix snp written 25 days ago by bigfoot0
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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 3 months 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 3 months ago by bigfoot0 • updated 3 months ago by Sam2.7k
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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 3 months ago by bigfoot0 • updated 3 months ago by Kevin Blighe59k
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Answer: A: METAL (gwas meta-analysis tool)
... I updated the software, now it works amazingly! ...
written 3 months 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 3 months 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 4 months 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 12 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 12 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 12 months ago by bigfoot0

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