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News: Cancer Genomics workshop
written by Physalia-courses 281Dear all, We are excited to announce our online course “Practical Somatic Variant Analysis in Cancer Genomics”, taking place 27–29 April. Course website: https://www.physalia-courses.org/courses-workshops/cg26/ This …
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Where to find hg38 panel-of-normals and germline VCFs without 'chr' prefix?
written by dpgpfkdkeldi 0I’m currently performing somatic variant calling with Mutect2 using hg38 as the reference genome. However, my BAM files were aligned using a version of the …
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Somatic variant filtering necessary files
written by Anitha 1Hello, As I am new to the GATK pipeline, I have some questions regarding the supplement file used for the somatic variant filtering step. I …
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How to extract the mutations specific to cancer after variant annotation
written by sainavyav22 0Hello, I am working on B cell lymphoma of dogs to identify the specific type of mutations related to this disease. I am performing NGS …
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GATK Mutect2 tumor mode
written by cocchi.e89 30I am working on some human WGS tumor samples and I want to call somatic variants against the normal tissue sample. I see that Mutect2 …
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Mutect2 "somatic" variants with resistant tissue culture lines
written by shawn.w.foley 130Hello! I'm trying to establish an analysis pipeline for whole exome seq (WES) of a cancer cell line with acquired resistance. In this experiment we …
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Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
written by sktbanerjee1 3I am trying to call variants from whole exome paired end sequences aligned to HG38p7 using the Freebayes variant caller. As it is a general …
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COSMIC vcf file compatibility for Mutect2
written by erwan.scaon 97I am running a variant calling pipeline for cancer samples. It includes Mutect2. Working on human, i started with the reference & dbsnp files contained …
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The problem with sensitivity analysis of somatic variant caller
written by phongphak.06 2Hello! I'm working on somatic variant identification from cancer samples. So, I try to simulate Illumina paired-end read with known variants by using VarSim (http://bioinform.github.io/varsim/), …
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Somatic and Germline variant calling in ion torrent
written by inayat45shaikh 4Hello, We have data of tumor (Tissue) and Normal (Blood) control from the same patients. We want to call somatic and germline variants in the …