close

Вход

Забыли?

вход по аккаунту

?

3107411.3108203

код для вставкиСкачать
Poster Session
ACM-BCB’17, August 20–23, 2017, Boston, MA, USA
Pisces: An Accurate and Versatile Single Sample Somatic
and Germline Variant Caller
Tamsen Dunn
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
tdunn@illumina.com
Yu Jiang
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
yjiang2@illumina.com
Gwenn Berry
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
gberry@illumina.com
Anita Iyer
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
aiyer@illumina.com
Dorothea Emig-Agius
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
dagius@illumina.com
Nitin Udar
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
nudar@illumina.com
Michael Strömberg
Illumina Inc.
5200 Illumina Way
San Diego, CA 92122
mstromberg@illumina.com
ABSTRACT
sample is of particular importance to research. Current state of
the art variant callers such as GATK and VarScan focus on
germline variant calling (used for detecting inherited mutations
following a Mendelian inheritance pattern) or, in the case of
FreeBayes and MuTect, focus on tumor-normal joint variant
calling (using the normal sample to help discriminate low
frequency somatic mutations from back ground noise).
We present Pisces, a tumor-only variant caller exclusively
developed at Illumina for detecting low frequency mutations from
next generation sequencing data. Pisces has been an integral part
of the Illumina Truseq Amplicon workflow since 2012, and is
available on BaseSpace and on the MiSeq sequencing platforms.
Pisces has been available to the public on github, since 2015.
(https://github.com/Illumina/Pisces)
CCS CONCEPTS
The Pisces variant calling team have developed Pisces as a method
for single-sample variant calling for tumor-only and germline
samples. We have made available a suite of variant calling tools,
including a ReadStitcher, Variant Phaser, and Variant Quality
Recalibration tool, to be used along with the core variant caller,
Pisces. In our poster, we describe the Pisces variant calling tools
and core algorithms.
• Applied computing~Computational genomics
KEYWORDS
Pisces; single sample; somatic; germline; variant caller; tumor
only
1 SUMMARY
A method for robustly and accurately detecting rare DNA
mutations in tumor samples is critical to cancer research. Because
many clinical tissue repositories have only FFPE-degraded tumor
samples, and no matched normal sample from healthy tissue
available, being able to discriminate low frequency mutations
from background noise in the absence of a matched normal
Permission to make digital or hard copies of part or all of this work for personal or
classroom use is granted without fee provided that copies are not made or distributed
for profit or commercial advantage and that copies bear this notice and the full
citation on the first page. Copyrights for third-party components of this work must
be honored. For all other uses, contact the owner/author(s).
ACM-BCB '17, August 20-23, 2017, Boston, MA, USA
© 2017 Copyright is held by the owner/author(s).
ACM ISBN 978-1-4503-4722-8/17/08.
http://dx.doi.org/10.1145/3107411.3108203
595
Документ
Категория
Без категории
Просмотров
2
Размер файла
493 Кб
Теги
3108203, 3107411
1/--страниц
Пожаловаться на содержимое документа