Tag: MUTECT2

Genomic hypomethylation in cell-free DNA predicts responses to checkpoint blockade in lung and breast cancer

Lung cancer ICB cohort Advanced non-small cell lung carcinoma patients who were treated with anti-PD-1/PD-L1 monotherapy at Samsung Medical Center, Seoul, Republic of Korea were enrolled for this study. The present study has been reviewed and approved by the Institutional Review Board (IRB) of the Samsung Medical Center (IRB no….

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GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data

GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data 0 Dear all, Is there any best practice for the mouse snp indel vcf files using GATK Mutect2 for mouse whole exome data? For mm10, it seems have several available, for mm39, it seems the newest is from…

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Detecting somatic variants in non-tumor tissue without normals

I’m new to genome analysis, so apologies if this is a basic question. My hypothesis is that in a particular disease, gene XYZ contains somatic mutations. I have performed targeted sequencing of gene XYZ with very high coverage using Sureselect. I have sequenced the gene in brain tissue from diseased…

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MemVerge and Sentieon Announce WaveRider for Sentieon to Accelerate Next-Generation Sequencing in the Cloud

Early Customers Realize 10x Increase in Performance and Cloud Cost Savings; Sentieon Software Offered Free in Memory Machine Cloud Subscription MILPITAS, Calif., Nov. 14, 2023 /PRNewswire/ — MemVerge®, pioneers of Big Memory software, and Sentieon®, the market leader in genomics software, today announced a collaboration to accelerate next-generation sequencing (NGS)…

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Correction of a homoplasmic mitochondrial tRNA mutation in patient-derived iPSCs via a mitochondrial base editor

Human induced pluripotent stem cells (iPSCs) Reprogramming and Culture This study was ethically approved by the Medical Ethics Committee of Nanjing Maternal and Child Health Care Hospital (2021KY-131), and informed consents were obtained from the patient’s legal guardian as well as the healthy donors, in accordance with the Declaration of…

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Bioinformatics Specialist I | MGH Cancer Center

!*! GENERAL SUMMARY/ OVERVIEW STATEMENT: In Gulhan Lab, we develop statistical and machine learning methods for cancer genomics to improve patient classification and early cancer detection strategies. We aim to decipher the broad spectrum of genomic instabilities that dictate the evolution of cancer genomes, and to understand how best to…

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Issues with FilterRNAMutationsNoPoN in RNA-Mutect Workflow for Tumour Mutational Burden Estimation

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…

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Is a PON necessary for tumor-normal matched Mutect2?

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…

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sarek: Introduction

Introduction nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is built using…

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Multiparameter prediction of myeloid neoplasia risk

Data acquisition UKB is a large-scale biomedical database and research resource containing genetic, lifestyle and health information from half a million UK participants. UKB has approval from the North West Multicentre Research Ethics Committee (11/NW/0382) and all participants provided written informed consent. The present study has been conducted under approved…

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gatk – A bash script for running on a bunch of bam files

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I googled and I realised for one function, I can do this cd /data/Continuum/WES/vcf/ for file in *.bam ; do ./gatk CollectSequencingArtifactMetrics -I /data/Continuum/WES/results/NG-27280_CLTSS_LTS_0017_lib506243_7661_2_MarkedDup.bam -O NG-27280_CLTSS_LTS_0017_lib506243_7661_2_MarkedDup –FILE_EXTENSION .txt -R resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta done;…

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Nuclear genetic control of mtDNA copy number and heteroplasmy in humans

Overview of mtSwirl Here we develop mtSwirl, a scalable pipeline for mtCN and variant calling which makes calls relative to an internally generated per-sample consensus sequence before mapping all calls back to GRCh38. In addition to GRCh38 reference files and WGS data, the mtSwirl pipeline takes as input nuclear genome…

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Massachusetts General Hospital hiring Bioinformatics Specialist I in Boston, MA

General Summary & Overview StatementThe Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our team…

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MutSigCV Input file

MutSigCV Input file 0 I am studying about driver gene. when i use the MutSigCV, require “coverage table file” and “covariates table file”. I want to know more about coverage table file. It has been confirmed that Mutect2 is used. But more explanation is needed. Thank you. MutSigCV Mutect2 drivergene…

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GATK GetPileupSummaries Java heap space

GATK GetPileupSummaries Java heap space 1 I am using GATK GetPileSummaries in the following way: GENOME=”/FILES/HUMAN_REFERENCES/hg19.fa” RECBAM=”/FILES/${patient_id}/${patient_id}.recalibrated.bam” intervals_list=”/FILES/HUMAN_REFERENCES/wgs_calling_regions.v1.interval_list” GERM=”/FILES/HUMAN_REFERENCES/small_exac_common_3-hg19.vcf” PON=”/FILES/HUMAN_REFERENCES/Mutect2-WGS-panel- b37-hg19.vcf”export GERM=”/FILES/HUMAN_REFERENCES/af-only-gnomad-hg19.raw.sites.vcf” VCF=”/FILES/${patient_id}/${patient_id}.recalibrated.vcf” OUTPUT=”/FILES/${patient_id}/${patient_id}.getpileupsummaries.table” srun /mnt/beegfs/apptainer/images/gatk4.sif gatk GetPileupSummaries \ -I $RECBAM \ -L $GERM \ -O $OUTPUT \ -V $GERM Resulting in the following error: 16:37:40.248 INFO NativeLibraryLoader – Loading…

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GATK GetPileUpSummariesUsage

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…

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PON and germline files for Mutect2 Tumor-only mode

Hi! I am applying Mutect2 in tumor-only.mode having hg19 as reference and samples resulting of targeted sequencing (not only coding gene parts but also some non coding regions), I found this: console.cloud.google.com/storage/browser/gatk-best-practices/somatic-b37%2F;tab=objects?prefix=&forceOnObjectsSortingFiltering=false. This bundle is used for b37 which is equivalent to hg19 (not 100% similar). export PON=”/filepath/Mutect2-WGS-panel-b37-hg19.vcf” export GERM=”/filepath/af-only-gnomad-hg19.raw.sites.vcf”…

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Convert files made for b37 into hg19 human reference?

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…

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Evolutionary histories of breast cancer and related clones

Data reporting No statistical methods were used to determine the sample size. The experiments were not randomized. Pathologists were blinded to the genetic alterations in each sample during histopathological evaluation. Participants and materials We enroled 207 female patients with breast cancer who underwent surgery at the Kyoto University Hospital and…

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GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.

Hi, I am following the GATK best practices pipeline for variant calling starting from targeted sequencing bam and bai files using the hg19 reference. When applying GATK Mutect2 got the following error A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found. reference…

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Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer

Baseline characteristics We described the baseline clinical and pathological characteristics of TNAC and LK-TNBC in Supplementary Table 1. Only stage at diagnosis was different between TNAC and LK-TNBC (P = 0.03), while no significant differences were observed in other characteristics, including nuclear grade, histologic grade, Ki-67, and status of (neo)adjuvant treatment. Somatic…

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Mutect2 error – Cannot construct fragment from more than two reads

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….

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GenomicsDBImport from Mutect2 output

I am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with: gatk Mutect2 \ -R ${REF} \ -L ${EXOME_INPUT_INTERVALS} \ -I ${BAM} \ –sequence-dictionary ${DICT} \ –max-mnp-distance 0 \ -O ${SAMPLE_NAME}.mutect2.vcf but I see that the tool is unable…

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Issue Running SomaticCombiner

Issue Running SomaticCombiner 0 Hi! I have been trying to run this software to combine the mutation calls from software Mutect2 and MuSE from a single sample, but have been running into issues. I checked that both vcfs are not empty. Here is a screenshot of the output. Does anyone…

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Massachusetts General Hospital hiring Bioinformatics Specialist I in Boston, Massachusetts, United States

General Summary & Overview StatementThe Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our team…

Continue Reading Massachusetts General Hospital hiring Bioinformatics Specialist I in Boston, Massachusetts, United States

Bioinformatics Specialist I – Massachusetts General Hospital(MGH)

GENERAL SUMMARY & OVERVIEW STATEMENT: The Iafrate Lab conducts pioneering research in the field of clinical genomics, working to develop personalized approaches to early cancer detection, diagnosis, and therapy. We are seeking a highly motivated bioinformatician with a background in statistics and/or software development to be a part of our…

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Which type of variant caller should I use in a WES normal cell line sample?

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…

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Inquiry Regarding Somatic Analysis and Normal Sample Requirement

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…

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Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files

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….

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Significance of “orientation” flag in FilterMutectCalls output

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…

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Somatic variant calling mutect2 ctDNA liquid biopsy

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…

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combine/merge closet variants into one from mutect2

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…

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WES variant calling with DNBSEQ-T7

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…

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Error while running GATK4 Mutect2 in Galaxy

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…

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Optimal approach for variant calling with 3 diluted germline sample in one sequencing

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…

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best pipeline/practice for analyzing WES for germline and somatic variant calling

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…

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Mutect2 MultiSample VCF out file

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….

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Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2)

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…

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GATK Mutect2 tumor mode

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…

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bcftools isec output for multiple vcf files interpretations

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…

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SV tool recommandation for detecting 50bp> deletion sequence

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…

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Apple M1 processor for bioinformactics

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?…

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Powering Toxicogenomic Studies by Applying Machine Learning to Genomic Sequencing and Variant Detection

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 …

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Filetering low reads from vcf file/ download exonic region, coding regions of GRCh38

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…

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mutect2 github – Iskanje Google

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…

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How to calculate tumor mutation burden (TMB)?

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…

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What sequencing/alignment artifact is this?

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…

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GDCquery_Maf error

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…

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A genomic mutation spectrum of collecting duct carcinoma in the Chinese population

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…

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Cancer Mutation Detection Depends on Choices at Each Step of Sequencing, Analysis Pipeline

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…

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Separate vcf file creation for matched tumor-normal samples

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…

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GATK CalculateContamination – zeros in output

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…

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Gene mutation analysis in papillary thyroid carcinoma

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…

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Contig chr1 given as location, but this contig isn’t present in the Fasta sequence dictionary

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…

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Mapping quality and XS score

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…

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