More posts like this
-
how to extract variants from the vcf.gz files linked below?
written by Mahad •I have tried several commands to extract the variant (non-homozygous) genotype from the two vcf.gz files found below, but no variant genotypes are coming up. …
-
difference between different field info in vcf file format
written by rheab1230 •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 …
-
NS, AC, AN and AF in VCF file
written by wangdp123Hi there, I am working with some VCF files and I find it difficult to understand some of the tags in the INFO column of …
-
Simulate offspring's genotype from parental genotypes (SNPs)
written by MH85 •Hi everyone, I have genotypes of mother and father in vcf (200 loci) and I want to simulate possible genotypes of their progenies. Is there …
-
Genotype concordance for vcf.gz
written by catarinaglmg •Hi! Does anyone know any tool that allows to compare genotypes between two compressed vcf files (.vcf.gz)? (Or any ideas how can I do it …
-
SNP genotyping from low-quality ddRADseq data
written by guilfon •Hello, I am working with ddRADseq data from harbor seal scat samples. There are not a lot of highly informative SNPs in my final panel …
-
VCFtools. Get rid of DS:GP phased genotypes while keeping GT and remaining fields
written by Mr LocuaceHello, I have a question about VCFtools I have a vcf file with the usual 9 columns in addition to phased data of several samples. …
-
Extract several fields from vcf file
written by kelly.wang135Hello all, I'd like to modify my vcfs to contain several info only. There are "GT:AD:DP:FT:GQ:PL:PP" in format column, but I want to include "GT,DP,GQ" …
-
Down-sample to one read per SNP loci per sample
written by aylward.megan •Does anyone know if there is a way of downsampling to a coverage of 1x per sample at known SNP loci? I have tried GATK …
-
VCF genotype generator
written by vigprasudDoes someone know of a software that can simulate genotypes for a variant with AC and AN counts, given a set of variants? I am …