Tag: Varscan

Tool:open-cravat: variant annotation tool 3 open-cravat is an open-source platform for rapidly developing, using, and disseminating variant annotation tools. It can handle unlimited number of variants in VCF format input files as well as its own input format and produce tab-separated text output files and excel spreadsheets. It is command-line-based…

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….

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the leading causes of death worldwide and caused 1.6 million deaths and 10.6 million new cases in 2021.1 Despite decades of efforts to adopt measures to control TB, achieving the goal of ending TB has been delayed due to a…

cfsan snp pipeline 1 I am using cfsan_snp_pipeline. The link of the git is- I have installed all the dependencies and install the pipeline via conda. when I execute the command- echo $CLASSPATH /home/saiful/home/saiful/Downloads/picard-2.18.2.jar:/home/saiful/home/saiful/Downloads/VarScan.v2.3.9.jar:/home/saiful/home/saiful/Downloads/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar: when I run the pipeline, cfsan_snp_pipeline run genomic.fasta -o cfsan_pipeline -s listeria Checking dependencies… CLASSPATH is…

How to plot venn diagram from vcf-compare output ? 1 i get the following output from vcf-compare by comparing two VCF : VN 2172 NA12878/intersect2.vcf.gz (6.8%) VN 29648 Coriell.varscan.snp.vcf.gz (20.7%) NA12878/intersect2.vcf.gz (93.2%) VN 113680 Coriell.varscan.snp.vcf.gz (79.3%) I would like to plot a Venn diagram quickly. Any idea ? Online tool…

ABSOLUTE for tumour purity with WES 0 Hello, I have WES paired data (tumour and normal) from Illumina sequencing and I would like to obtain a purity score. ABSOLUTE seemed perfect but I can’t get it to work. Here’s my workflow: Generate .pileup from .bam with SamTools Generate .copynumber from…

Harden, V. A. Rocky mountain spotted fever: History of a twentieth-century disease Vol. 16 (Johns Hopkins University Press, 1990). Google Scholar  Maxey, E. E. M., G T; Leary, J W. (1899) Some observations on the so-called spotted fever of Idaho. Med Sentinel, 7: 433–438. Dantas-Torres, F. Rocky mountain spotted fever….

Schumacher, T. N. & Schreiber, R. D. Neoantigens in cancer immunotherapy. Science 348, 69–74 (2015). Article  ADS  CAS  PubMed  Google Scholar  Tran, E., Robbins, P. F. & Rosenberg, S. A. Final common pathway’ of human cancer immunotherapy: targeting random somatic mutations. Nat. Immunol. 18, 255–262 (2017). Article  CAS  PubMed  PubMed…

Obtaining bcf and vcf files and use bcf tool annotate 1 I have vcf file that I obtained from the galaxy and I want to run bcftools annotate. I ran the following command: bcftools annotate -a Galaxy96-\[Galaxy45-\[VarScan_on_data_44\].vcf\].vcf -o samtools_annotated.vcf But no output file is generated? How can I use different…

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 …

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…