mark duplicates (picard) (Broad Institute Inc)

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Broad Institute Inc mark duplicates (picard)
Mark Duplicates (Picard), supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/picard+mark+duplicates/picardtools++mark+duplicates/pm40223084-72-6-9
Average 90 stars, based on 1 article reviews

mark duplicates (picard) - by Bioz Stars, 2026-10

90/100 stars

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Article Title: VHL mosaicism: the added value of multi-tissue analysis.
Article Snippet: Duplicate reads were marked (Picard Mark Duplicates; version 1.130) and the Genome Analysis Toolkit (version 3.3.0; Broad Institute, Cambridge, MA) best practices followed Base Quality Score Recalibration.

Article Title: Molecular yield and cytomorphologic assessment of fine needle aspiration specimen supernatants.
Article Snippet: Introduction Cytology samples are frequently relied upon for the diagnosis of advanced cancer such as lung cancer.. As the recommendations for solid malignancies biomarker testing continue to expand, it becomes increasingly important to efficiently utilize limited specimens to minimize the need for additional sampling and its associated risks and costs.. Materials and methods We performed molecular testing on fresh or CytoLyt-fixed supernatants derived from fine needle aspirates (FNAs) and compared its performance against the clinical specimen (including formalin-fixed paraffin-embedded cell blocks, residual PreservCyt and fresh samples).

Article Title: Whole exome sequencing of a family revealed a novel variant in the <i>CHM</i> gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia
Article Snippet: Base quality was recalibrated by Picard Mark Duplicates (http://sourceforge.net/projects/picard/), Genome Analysis Toolkit (https://gatk.broadinstitute.org/hc/en-us), and SAM tools (http://samtools.sourceforge.net/) [22].

Article Title: Validation of BRCA testing on cytologic samples of high-grade serous carcinoma.
Article Snippet: BACKGROUND: Testing for BRCA1/2 gene alterations in patients with highgrade serous carcinoma (HGSC) is a critical determinant of treatment eligibility for poly(adenosine diphosphateribose) polymerase inhibitors in addition to providing vital information for genetic counselling.. Many patients present with effusions necessitating therapeutic drainage, and this makes cytologic specimens (CySs) the initial diagnostic material for HGSC, often before histologic sampling.. Initiating somatic BRCA testing on a CyS allows the BRCA status to be determined sooner, and this affects clinical management.

Article Title: Tumor and germline next generation sequencing in high grade serous cancer: experience from a large population‐based testing program
Article Snippet: Duplicate reads were marked using Picard Mark Duplicates (Broad Institute, Cambridge, MA, USA) followed by application of the Genome Analysis Toolkit ( gatk v3.3‐0) best practices recommendations (Broad Institute) for Base Quality Score Recalibration ( bqsr ) algorithm.

Article Title: Whole exome sequencing of a family revealed a novel variant in the CHM gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia
Article Snippet: Base quality was recalibrated by Picard Mark Duplicates ( http://sourceforge.net/projects/picard/ ), Genome Analysis Toolkit ( https://gatk.broadinstitute.org/hc/en-us ), and SAM tools ( http://samtools.sourceforge.net/ ) [ ].

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Article Title: Whole Exome Sequencing Revealed Three Novel Variants in TSPAN12 and LRP5 Genes for Two Families with Familial Exudative Vitreoretinopathy
Article Snippet: .. Quality control was recalibrated by Picard Mark Duplicates (http://sourceforge.net/projects/picard/), Genome Analysis Toolkit (https://gatk.broadinstitute.org/hc/enus), and SAM tools (http://samtools.sourceforge.net/). .. Variants were validated and analyzed preferentially if they met the following previously reported criteria (24–26): (1) minor allele frequency of the variant < 0.01 in the 1000 Genomes Project database (http://www.internationalgenome.org/), Exome Aggregation Consortium database (http://exac.broadinstitute.org/), Genome Aggregation database (http://gnomad.broadinstitute.org/), and an in-house Chinese individuals database; (2) variant location in an exon region or canonical splicing intron region that affected transcription splicing; (3) damaging or deleterious variant prediction using Sorting Intolerant From Tolerant (http://sift.jcvi.org/), Polymorphism Phenotyping (http://genetics.bwh.harvard.edu/pph2/), ClinPred (https://sites.google.com/site/clinpred/), Likelihood Ratio Test (http://www.genetics.wustl.edu/j ab/lrt), Mutation Taster (http://www.mutationtaster.org/), Mutation Assessor (http://mutationassessor.org/r3), Functional Analysis Through Hidden Markov Models (http://fathmm.biocompute.org.uk/), and Protein Variation Effect Analyzer (http://provean.jcvi.org); (4) highly conserved variant prediction using Genomic Evolutionary Rate Pro ling (http://mendel.stanford.edu/SidowLab/downloads/gerp); (5) other reported pathogenic variant that did not meet the above criteria (e.g., high minor allele frequency variant, deep-intronic variant, or synonymous single nucleotide variant).

Article Title: Whole exome sequencing revealed 14 variants in NDP, FZD4 , LRP5, and TSPAN12 genes for 20 families with familial exudative vitreoretinopathy
Article Snippet: .. Quality control was recalibrated by Picard Mark Duplicates ( http://sourceforge.net/projects/picard/ ), Genome Analysis Toolkit ( https://gatk.broadinstitute.org/hc/en-us ), and SAM tools ( http://samtools.sourceforge.net/ ). .. Variants were validated and analyzed preferentially if they met the following previously reported criteria [ – ]: (1) minor allele frequency of the variant < 0.01 in the 1000 Genomes Project database ( http://www.internationalgenome.org/ ), Exome Aggregation Consortium database ( http://exac.broadinstitute.org/ ), Genome Aggregation database ( http://gnomad.broadinstitute.org/ ), and an in-house Chinese individuals database; (2) variant location in an exon region or canonical splicing intron region that affected transcription splicing; (3) damaging or deleterious variant prediction using Sorting Intolerant From Tolerant ( http://sift.jcvi.org/ ), Protein Variation Effect Analyzer ( http://provean.jcvi.org ), Polymorphism Phenotyping ( http://genetics.bwh.harvard.edu/pph2/ ), ClinPred ( https://sites.google.com/site/clinpred/ ), Likelihood Ratio Test ( http://www.genetics.wustl.edu/jflab/lrt ), Mutation Taster ( http://www.mutationtaster.org/ ), Mutation Assessor ( http://mutationassessor.org/r3 ), and Functional Analysis Through Hidden Markov Models ( http://fathmm.biocompute.org.uk/ ); (4) highly conserved variant prediction using Genomic Evolutionary Rate Profiling ( http://mendel.stanford.edu/SidowLab/downloads/gerp ); (5) other reported pathogenic variant that did not meet the above criteria (e.g., high minor allele frequency variant, deep-intronic variant, or synonymous single nucleotide variant).

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