Tag: MuTect

BWA mem -M option for gatk mutect 0 Hi, everyone! I am new to the gatk pipelines, so I’m not sure is it necessary to use the -M option in the bwa men commond before I put the outcoming bam file to the gatk mutect pipelines for calling the mutation…

Issues with FilterRNAMutationsNoPoN in RNA-Mutect Workflow for Tumour Mutational Burden Estimation 0 Hello community, I am currently working on estimating tumour mutational burden using the RNA-Mutect-WMN pipeline. The process requires an output from RNA-Mutect, which in turn needs the output of Mutect2. I have proceeded with the following steps: Acquired…

Is a PON necessary for tumor-normal matched Mutect2? 1 I’m a bit confused on whether or not i should include GATK’s public PON (either 1000g_pon.hg38.vcf.gz since I aligned with hg38), make my own from my normal samples, or just leave it and not include a PON. I am planning on…

GATK GetPileUpSummariesUsage 0 Hi, I am doing variant calling using as reference hg19. After Gatk Mutect with PON Mutect2-WGS-panel-b37.vcf transformed into Mutect2-WGS-panel-b37-hg19.vcf and germline af-only-gnomad.raw.sites.vcf to af-only-gnomad.hg19.raw.sites.vcf (with Picard LiftOver). After doing Mutect2 next step is GATK GetPileUpSummaries, that has this usage from GATK website: gatk GetPileupSummaries \ -I tumor.bam…

Hi everybody, A bam file has been aligned using hg19 reference genome. Thus, the chromosome notation is [chrM, chr1, chr2, chr3, chr4, …, chrX,chrY]. I want to look for PMs using MuTect that requires in input vcf files from dbSNP and COSMIC. In these vcf files the chromosome notation is…

Convert files made for b37 into hg19 human reference? 1 Altough hg19 and b37 being considered similar they have some differences that affect the pre processing when doing variant calling. Is there any tool to convert the references for panel of normals or know-sites that are applied in Mutect for…

Mutect2 error – Cannot construct fragment from more than two reads 0 Hi, I’m trying to analyze WGS data and I’m currently running Mutect2, however, I’ve been receiving the following error message stating “Cannot construct fragment from more than two reads” and I’m not sure where things have gone wrong….

compression of FASTQ files 0 I want to merge fastq files of the same sample sequence in two different times, one file is .gz and the second is .qp. i did merge them with “cat file1.gz file2.gz file3.gz > allfiles.gz” and the out file is either .qp or .gz. However,…

Somatic variant calling mutect2 ctDNA liquid biopsy 0 Hi! I am trying to call ctDNA somatic variants in a sample that comes from liquid biopsy of a cancer patient. I also have a healthy control that comes from an in-house plasma sample. I want to apply mutect2 but I have…

We are seeking a bioinformatician with significant oncology or immunology experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system’s response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics…

What sequencing/alignment artifact is this? 0 I’m calling mitochondria variants with mutect2 and one variant looks like an artifact but I don’t understand what could be the cause. It looks like from IGV (picture below) that this variant is always at the same position on forward and backward reads. Also…

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

Bowtie2 hg19 reference for gatk MuTect 3 Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and…