According to GATK best practice, it is recommended that different VQSR models be built for SNPs and INDELs, because the annotations for high-quality SNPs and …

Dear community members, I need to genotype 6 millions of array markers from a BAM WGS file. It works perfectly for substitutions, e.g., ref allele …

I am using Eage to phase plink input. I maintain --keep-allele-order throughout my workflow. Eagle outputs .haps (Oxford phased haplotype file), which I convert to …

I've got VCF-like files with start, stop, REF and ALT columns. I need to check that the REF position from the variants are the same …

I'm trying to include only single nucleotide variant, or some say SNPs, from the 1000 genomes project data. (For example, the phase 3 newest release …

I want to run some tests on the 1000 Genomes project Phase 3 VCF files: I downloaded the files from here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ From these files …

<p>This builds on prior question <a href="http://www.biostars.org/post/show/11990/genotype-data-and-exome-sequencing-data-sensitivity/">http://www.biostars.org/post/show/11990/genotype-data-and-exome-sequencing-data-sensitivity/</a></p> <p>If I care only about variants covered by dbSNP with an rsXYZ number and assuming I could do …

<p>Do you know of any tool that can convert VCF format for variant calls to GATK verbose style format (Start and stop coordinates with insertion …

<p><strong>Background:</strong> Usually we grouped the genomic variants into different types, like SNP, insertion, deletion, Transposable element.</p> <p>I would like to get some primary statistics, like …

<p>I have vcf files with genomic variants (e.g. SNPs and Indels) from several patients. I now want to merge them into one vcf file e.g. …