Hello, I have 2 VCFs resulting from different imputation (same tool but using different sources for reference genomes); while one of the imputed files generally …

Edit: See answer. tl;dr: code should have been: plink2 --vcf [input-name] dosage=HDS --exclude-if-info "R2<=0.3" --export vcf --out [output-name] **Original post** I'm struggling with post-imputation processing …

Hello, Does anyone know what the difference between these two field format in vcf file. GT vs DS. I know GT represent genotype information and …

After running PLINK --lasso command with an h2 estimate 0.8, I received a plink.lasso; however, I am a little confused on how that file is …

Hi! I want to filter a sam file (produced by bowtie2) based on alignment score (column 14) >= 5000. I tried: awk '{ if($14 >= …

Hi, I have just downloaded imputation result files from the Michigan Imputation Server. The files include ".info.gz" and ".dosage.gz". I will like to filter the …

Would be very grateful for help. I have a VCF.gz file for imputed SNP data. I know for a fact that this file contains imputation …

Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz Michigan imputation server use …

How to subset a dosage file with a custom list of variants? I need to extract the dosage information for a subset of variants from …

<p>Hi,</p> <p>I have summary statistics from association studies with data imputed using different softwares, IMPUTEv2 and Minimac. I am having trouble understanding whether the two …