Tag: MUTECT2

Which type of variant caller should I use in a WES normal cell line sample? 0 I have whole-exome sequencing data of an immortalised non-tumor (normal) cell line that I wish to assess for the presence/absence of APC/Wnt mutations. This is to double check that the cell line is sufficiently…

Inquiry Regarding Somatic Analysis and Normal Sample Requirement 1 Dear All, I have two questions: I plan to perform somatic analysis on 10 different tumor BAM files to determine the SNPs, indels, and CNVs. Is it necessary to have 10 distinct normal files corresponding to each tumor BAM file, or…

Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files 0 Leung et al., 2017 paper mentioned in Fig 1 data processing for CRC patients was sequenced as single cell for both SNV (with MDA WGA) and CNA (with DOP-PCR) parallelly….

Significance of “orientation” flag in FilterMutectCalls output 0 Hi! I have an annotated vcf file generated by mutect2 and flagged by FliterMutectCalls. Thing is, I have found my variant of interest but it is not flagged as PASS but as “orientation”. I want to know if the read orientation bias…

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…

Using GATK Mutect2, we collected several variants in EGFR region. However, one variants NM_005228.5(EGFR):c.2239_2248delinsC (p.Leu747_Ala750delinsPro) were called as two separated ones. The two variants can not combined even we set the -max-mnp-distance to 20. 7 55242465 . GGAATTAAGA G . .AS_SB_TABLE=5567,5732|44,36;DP=11794;ECNT=2;MBQ=20,20;MFRL=188,168;MMQ=60,60;MPOS=39;NALOD=3.85;NLOD=1755.82;POPAF=4.52;TLOD=256.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB0|1:2957,80:0.027:3037:1304,28:1306,51:0|1:55242465_GGAATTAAGA_G:55242465:1402,1555,44,36 0|0:8342,0:1.710e-04:8342:3598,0:4195,0:0|1:55242465_GGAATTAAGA_G:55242465:4165,4177,0,0 7 55242478 . G C . .AS_SB_TABLE=5360,5529|44,36;DP=11030;ECNT=2;MBQ=20,20;MFRL=189,168;MMQ=60,60;MPOS=43;NALOD=3.93;NLOD=1686.18;POPAF=4.52;TLOD=256.12…

WES variant calling with DNBSEQ-T7 – technical quality assessment 0 Hi everyone! I recently received whole exome sequencing samples that were sequenced on an MGI sequencing instrument, DNBSEQ-T7. I am interested in somatic variant-calling on the paired tumor-normal samples. As this isn’t the canonical Illumina sequencer, an issue that I…

Error while running GATK4 Mutect2 in Galaxy 1 I have one clown and one control sample of python molurus bivittatus. After alignment, I am trying to use GATK4 Mutect2 to joint variant calling: But after executing I got this error: A USER ERROR has occurred: Bad input: The given bam…

Forum:Optimal approach for variant calling with 3 diluted germline sample in one sequencing – Capture Sequencing 0 Hello everyone, I have to analyse Capture Sequencing 170 genes in a type of cancer. We have 75 tumors sequenced individually and 45 matched germline of good quality. I have to do a…

best pipeline/practice for analyzing WES for germline and somatic variant calling 1 I haven’t been doing variant calling for a long while and now I got a new project that I’ll be doing some variant calling on cancer patient normal and tumor samples. I’m interested in calling both germline variants…

Circos plot using vcf : Mutect2 MultiSample VCF out file 0 Hi I have multisample vcf out file from Mutect2 and would like to make circos plot showing variants in multiple sample. Any suggestions or directions please ? Mutect2 vcf file multisample • 76 views Login before adding your answer….

Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2) 0 gatk.broadinstitute.org/hc/en-us/articles/360036227652?id=4147 In the article it described the process of finding active regions. I found Downsampling step in final post-processing quite confusing. Could someone explain the reason for this step? There is a final post-processing step to clean up and trim the…

GATK Mutect2 tumor mode 2 I am working on some human WGS tumor samples and I want to call somatic variants against the normal tissue sample. I see that Mutect2 had a tumor-mode in previous Mutect2 (now deprecated) guidelines but I can not find it anymore in current GATK Mutect2…

bcftools isec output for multiple vcf files interpretations 0 I have four vcf files resulting from mutect2 function. There is one treatment and three control samples. I need to get variants that are unique to the treatment plus variants that are common in all four vcf files files(treatment and control…

SV tool recommandation for detecting 50bp> deletion sequence 0 Hello. I am a 1st year grad student in genetics lab. I am new to bioinformatics. computer: MS-Linux ubuntu-miniconda3 data: fish tissue gDNA NGS(MGISEQ,, 150 paried end read) picard bam, bai file My goals are 1. compare sample seq with NCBI…

Apple M1 processor for bioinformactics 3 Hi everyone, I am thinking about buying a new laptop for bioinformatics. The new Macbook Pro with M1 processor looks really powerful. But does anyone know if there is any compatible issues for bioinformatic softwares with the Apple M1? Is there any potential issues?…

Alexandrov LB, Nik-Zainal S, Wedge DC et al (2013) Signatures of mutational processes in human cancer. Nature 500:415–421. doi.org/10.1038/nature12477 CrossRef  CAS  Google Scholar  Alioto TS, Buchhalter I, Derdak S et al (2015) A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun 6:10001. doi.org/10.1038/ncomms10001 CrossRef  CAS …

Filetering low reads from vcf file/ download exonic region, coding regions of GRCh38 – hg38 1 I am analyzing variant calling on RNASeq data using somatic pipeline of mutect2 function in gatk. To fileter the resulting variants, I need to filter out low reads in a way that for example…

Piškotke in podatke uporabljamo za to: zagotavljanje in vzdrževanje Googlovih storitev; spremljanje izpadov delovanja in zaščito pred vsiljeno vsebino, prevarami in zlorabo; merjenje dejavnosti ciljnih skupin in statističnih podatkov glede spletnih mest zaradi razumevanja, kako se uporabljajo naše storitve, in izboljšanja kakovosti teh storitev. Če izberete »Sprejmi vse«, bomo piškotke…

How to calculate tumor mutation burden (TMB)? 0 Hi I’ve tumor-normal WES data and I’ve analyzed data using GATK-Mutect2 pipeline to call somatic mutations. Now can anyone let me know hoe to calculate tumor mutation burden or mutation rate of my samples? I’m not able to find out the base…

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…

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

This article was originally published here BMC Med Genomics. 2022 Jan 3;15(1):1. doi: 10.1186/s12920-021-01143-2. ABSTRACT BACKGROUND: Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In…

NEW YORK — An international team of researchers has examined how variations in sequencing approaches can influence the ability to accurately detect cancer mutations, providing guidance for the wider community. The team additionally developed a set of reference samples for benchmarking efforts. Next-generation sequencing approaches are increasingly being adopted to…

Separate vcf file creation for matched tumor-normal samples 0 I have received 8 matched normal tumor vcf files from our collaborators. For some reason, they didn’t provide the sequence bam files and called the variants themselves (by aligning with the reference hg19 genome for both pairs separately). Basically, I have…

GATK CalculateContamination – zeros in output 2 Hi, I am new to exome-seq and would be grateful for any suggestions 🙂 I want to run GATK CalculateContamination (GATK 4.1.8.1), before calling variants with MuTect2. CalculateContamination tool returns “SUCCESS” message, but with warnings, and I get only “0” values in my…

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn’t present in the Fasta sequence dictionary 2 Hi everyone, I’m trying to run Mutect2 for WES cancer data. However, since their Resource bundle only supports h19 seems I cannot proceed (I want to compare it with Strelka2…

Mapping quality and XS score 0 Hi, I am currently looking through bam files using igv to manually check if the mutations not called by Mutect2 are really an error or not. Until now, to filter reads with low quality, I have used only MAPQ > 30 and didn’t consider…