I am trying to implement a strategy to investigate mosaic loss of chromosome Y (mLOY) with some CNV caller that works on NGS data. I …

Hi there, I'm running gatk PostprocessGermlineCNVCalls for a cohort of hg19 aligned WES samples. I'm following the suggested pipeline here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-number-variants#5 However, in the final …

Hello all, I'm working with human WGS data from germline for rare disease. I'm a bit lost for the VQSR step because the command (option) …

I'm interested in finding the tool GATK4 ACNV to generate segmentation files to use with ABSOLUTE. This tool is mentioned here: https://gatk.broadinstitute.org/hc/en-us/articles/360035889651-Are-there-any-Broad-specific-instructions-for-using-GATK- and here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890011--How-to-part-II-Sensitively-detect-copy-ratio-alterations-and-allelic-segments …

Dear all, I am working on a pipeline that should include Copy Number Variation calling (next to variant calling and some other stuff). To test …

I was wondering about the theoretical differences and use-case applications for the 2 different GATK CNV calling pipelines: [germline][1] and [somatic][2] I know that the …

Hi everyone, I'm using the GATK germline short variant discovery (SNPs + Indels) pipeline. https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- After using HaplotypeCaller to call the GVCF, I'm not consolidating …

I am trying to run GATK CNV germline on some human hg19 WGS samples. I followed the passages reported in their [best-practice guidelines][1]. I started …

I am working on somatic calling using GATK Mutect2 and following their [best practice guidelines][1] they now have a CalculateContamination step whose example states: gatk …

Hi ! I was asked to determine the ploidy level and to do **CNV calling** on a **yeast sample** (Reference sequence : *S. cerevisiae* S288C). …