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. …

Hello all, I've been working with microarray data which, of course, explicitly reports the genotype at each SNP on the microarray chip Now I am …

Hello, I am currently trying to build a germline variant calling pipeline using GATK. One step is the [Variant quality score recalibration][1]. For this I …

Hi all I usually use Plink1.9 to deal with the genotype data for variant and individuals manipulation such as genotype extraction based on rsID locally …

Dear Friends, I am trying to find genotype markers using 1000 Genomes VCF file for the continents Africa, Europe and East Asia. I am not …

So, I've got a VCF file of my whole genome sequence. I've used vcftools and plink to convert it into a bed file I merge …

Hello, I am interested in obtaining haplotypes (and their frequencies) from a region of the human genome from a particular population from the Phase3 1000 …

<p>How can I download genotype of specific snp (snp of coding region) for African population from 1000 Genome?</p> <p>Thanks</p>

<p>I have two already phased vcf files(one patient and one control), and would like to merge them together.</p> <p>I've tried vcf-phased-joint, but it requires the …

<p>Hi all,</p> <p>I am interested in finding the difference in algorithms used by the tools gatk and <a href='http://samtools.sourceforge.net/'>samtools</a>.Although both of them use a bayesian …