Hi, I am using Mutect2 to generate VCF files from BAM files which were pre-processed using GATK's pipeline. I did not use the -germline-resource argument. …
Hi. Studing tool of RealginerTargetCreator, I'm faced with a curious problem. --known / -known Input VCF file with known indels Any number of VCF files …
Hi Biostars, I have generated vcf file from RNAseq data and reconstructed alternative haplotype using GATK HaplotypeCaller and FastaAlternateReferenceMaker, respectively. The latter one handles indels, …
<p>Hi all,</p> <p>I have DNA sequencing data where human tumors have mouse reads as per the experiment protocol(similar to PDX).</p> <p>I have calculated the read …
<p>Hi,</p> <p>I have a VCF file (which contains indels as well as SNPs) obtained from an individual's DNA (from a whole genome microarray) with respect …
<p>Hi,</p> <p>I have annotated my vcf file of 20 samples from Unified genotyper using the following steps.</p> <p>Unified genotyper->Variantrecalibration->Applyrecalibration->VariantAnnotator</p> <p>My question is how should I …