More posts like this
-
genome build for --extract bed1 file in PLINK
written by eosimo 0Hello all, I'm a PLINK newbie. I am trying to extract a number of SNPs from a large imputation bgen file using the plink commands …
-
Extracting variant counts from Gnomad genome VCFs
written by storm1907 3Hello, I need to extract counts of synonymous and functional variants from gnomad v.3.1 genomes https://gnomad.broadinstitute.org/downloads I already have downloaded these genomes, extracted only exomic …
-
How to retrieve the list of rsid from .bgen file?
written by garyzhubc 0How to retrieve the list of rsid from .bgen file? Is there a simple way in linux to browse .bgen file?
-
plink2 extract subset of samples from .bgen file
written by UMen 1Hi Biostars, I try to extract a subset of samples from a .bgen file using plink2. Output format should also be .bgen. Searched the manpages …
-
Not enough SNPs after filtering an imputed dataset
written by Max 2Hi, I am using qctool to filter variants from an imputed dataset (from UK Biobank). The imputed data contains 93095623 autosomal SNPs. My list of …
-
ref and alt allele count from BAM file
written by monaallouba 0Hi All, I would like to calculate the allele ratio of ref/alt at a specific position. How can I determine the ref and alt counts …
-
Strands are reversed
written by richyanicky 3Hello, I have converted a Ukbiobank bgen file to vcf for processing against a reference panel using beagle. to make the pgen file from bgen …
-
extracting Allele Read Counts
written by Bogdan 144Dear all, please could you advise : given a (tumor) BAM file and a (germline) VCF file, what tool shall i use in order to …
-
How to calculate the genetic risk score?
written by Mahan 7I have a SNP data which looks like SNP A SNP B SNP C AA GG CC AC CG GC etc How can I calculate …
-
How to get Allele Coverage from bam file or vcf file?
written by murali 11I am working with targeted sequencing, I want to find the allele coverage? What is the allele coverage, and how can I extract it from …