User: gradstudentNew

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Posts by gradstudentNew

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Complicated Multi-factor Differential Expression
... Hello all. Merry Christmas and happy holidays! I am currently conducting a study and was hoping to get some advice on my model for differential expression. Currently, I have the following data: Sample || Sex || Age || TissueType || Individual || Diseased ID1 || Male || 70 | ...
rnaseq multifactor sleuth differential expression written 6 months ago by gradstudentNew10 • updated 6 months ago by Charles Warden7.0k
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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 11 months ago by gradstudentNew10 • updated 11 months ago by chrchang5235.4k
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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. ...
gwas imputation summary statistics genotyping written 12 months ago by gradstudentNew10
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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 13 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 13 months ago by gradstudentNew10 • updated 13 months ago by Pierre Lindenbaum121k
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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 13 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 13 months ago by gradstudentNew10 • updated 13 months ago by genomax69k
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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 h ...
vcf exome question vcftools genotype written 13 months ago by gradstudentNew10 • updated 6 months ago by zx87547.7k

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