Evidence map›Paper›PMID 34341766›Full record

ArticleArXiv2021

Bam-readcount - rapid generation of basepair-resolution sequence metrics.

Ajay Khanna, David E Larson, Sridhar Nonavinkere Srivatsan, Matthew Mosior, Travis E Abbott, Susanna Kiwala, Timothy J Ley, Eric J Duncavage, Matthew J Walter, Jason R Walker and 3 more

Abstract readPreprint
In one paragraph

Article in ArXiv, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Ajay Khanna *Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
David E Larson *McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO.
Sridhar Nonavinkere SrivatsanDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
Matthew MosiorDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
Travis E AbbottMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO.
Susanna KiwalaMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO.
Timothy J LeyDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
Eric J DuncavageDepartment of Pathology, Washington University School of Medicine, St. Louis, MO.
Matthew J WalterDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
Jason R WalkerMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO.
Obi L GriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
Malachi GriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.
Christopher A MillerDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO.

Funding

Specimen Acquistition and Expression ProfilingP01CA101937 · NCI · WASHINGTON UNIVERSITY · PI LEY, TIMOTHY J. · 2003 to 2023
$58.8M
Standardized and Genome-Wide Clinical Interpretation of Complex Genotypes for Cancer Precision MedicineU24CA237719 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2019 to 2023
$3.8M
COMPREHENSIVE INFORMATIC ANALYSES OF AML GENOMES AND EPIGENOMESR50CA211782 · NCI · WASHINGTON UNIVERSITY · PI Christopher A Miller · 2017 to 2026
$1.5M
DEVELOPMENT OF INFORMATICS RESOURCES FOR INTERPRETATION OF CLINICALLY ACTIONABLE VARIANTS IN CANCERU01CA209936 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2016 to 2018
$1.0M
Integrated Analysis & Interpretation of Whole Genome Exome & Transcriptome SequenR00HG007940 · NHGRI · WASHINGTON UNIVERSITY · PI GRIFFITH, MALACHI · 2017 to 2019
$724k
DEFINING THE REGULATORY, NON-CODING, MUTATIONAL LANDSCAPE OF BREAST CANCERK22CA188163 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2014 to 2016
$515k
NCI NIH HHS K22 CA188163NCI NIH HHS P01 CA101937NCI NIH HHS R50 CA211782NCI NIH HHS U01 CA209936NCI NIH HHS U24 CA237719NHGRI NIH HHS R00 HG007940
6 · The paper itself

Abstract

Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant detection tools and for resolving ambiguity between variant callers

Identifiers

PMID34341766
PMCPMC8328062

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.