User: gradstudentNew

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Posts by gradstudentNew

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Keeping both A1/A2 in PLINK for assoc/logistic output
... Hey guys, I was wondering if there's anyway to keep both A1 and A2 in PLINK for the logistic output? I used to merge my freq. output and assoc output. However, since I use HWE / MAF filters, it only applies to the logistic and the merging no longer works since they're not in order anymore. Any su ...
gwas plink written 4 months ago by gradstudentNew10 • updated 3 months ago by chrchang5234.3k
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Best way to impute GWAS summary statistics
... Hi guys, I was wondering what the best way would be to impute GWAS summary statistics when you don't have individual genotyping data? Currently, I'm using ImpG but was curious whether there were any better ways to do this. ...
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Comment: A: Extracting genotypes and filtering from a VCF file containing multiple exomes of
... Thank you so much for the help! I'm trying to more so get my file to be like the following: FamilyID IndividualID rs1 rs2 rs3 rs4 rs5 ... rsN fam1 1 0/0 0/1 0/1 0/0 0/0 fam1 2 0/2 0/1 0/1 0/1 0/0 if that makes sense - kind of like your first example but a bit more parallel. The thing is, I have t ...
written 6 months ago by gradstudentNew10
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Extracting genotypes and filtering from a VCF file containing multiple exomes of families
... Hi all, I'm currently trying to extract genotypes from a VCF file but I'm not really sure how to approach this. This is how the data line looks like: 12 2224727 . C T 6204.77 PASS 0.0010 rs377534958 CACNA1C GT:AD:DP:GQ:PGT:PID:PL:SAC 0/0:5,0:5:12:.:.:0,12,180 ...
vcf filter exome dna-seq genotype written 6 months ago by gradstudentNew10 • updated 6 months ago by Pierre Lindenbaum115k
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Comment: C: Extracting certain columns from VCF file
... Hey guys, I ended up using some perl scripting to fix my issue. I realized that everything was being printed in the 9th column i.e. Exac|gnomad|..|..| so I ended up spliting that column and then pasting / joining the ones I needed. :) Thank you all for the help! ...
written 6 months ago by gradstudentNew10
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Comment: C: Extracting certain columns from VCF file
... I'm really new to bioinformatics, so thank you so much for your help! I tried doing that and it said that the column(s) didn't exist. I'm not sure whether it's because of how my VCF file is formatted? My info header looks like this: ##INFO= ...
written 6 months ago by gradstudentNew10 • updated 6 months ago by genomax59k
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Extracting certain columns from VCF file
... Hello all, I've been recently trying to extract only certain columns with vcftools of an annovar-run VCF file. I did the following command: vcftools --vcf file_ANNOVAR.vcf --recode-INFO ExAC_SAS_AF --recode-INFO rs_dbSNP147 --out OUTPUT.vcf but it unfortunately isn't working. Does any one have any ...
vcf exome question vcftools genotype written 6 months ago by gradstudentNew10 • updated 6 months ago by Kevin Blighe33k

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