STR expansion detection on IonTorrent WES data?
Hello there,
All the STR expansion softwares I've found that support WES do not support IonTorrent data.
Is there a program that support both of these?
Thanks in advance for your time and help!
repeat
str
iontorrent
wes
ngs
short
tandem
• 754 views
•
link
written
by
Joel Wallenius
22
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Linkage disequilibrium estimation in unphased data?
written by Joel Wallenius 22Hello there, I've been tasked to LD-prune a set of variants that my group is interested in. Our data is human WES, and it is …
-
WES and GBAP1
written by Joel Wallenius 22Hello, sequencing the GBA1 gene is important in hereditary Parkinson's disease research. Just upstream of GBA1 is a pseudogene GBAP1 with 90+ % sequence identity. …
-
What are the WES-specific settings when running GATK's variant recalibration step?
written by Joel Wallenius 22Hello, while reading GATK's article here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531112--How-to-Filter-variants-either-with-VQSR-or-by-hard-filtering ... they helpfully supply some default tranch values and suches for WGS data. They say that for WES …
-
Find ~1 Mb regions of genome that are shared by two or more WGS samples?
written by Joel Wallenius 22Hello, I have 12 WGS samples that are part of a big pedigree, I need to pinpoint genomic regions ~1 Mbp that are identical between …
-
Can you not phase exome data?
written by Joel Wallenius 22Hello! I'm just getting acquainted with softwares that phase variant calls. I tried SHAPEIT2, and am planning to try Beagle and SHAPEIT4. I'm working with …
-
"Best" freewares for linkage analyses?
written by Joel Wallenius 22Hello! I've been tasked to perform linkage analysis on some data we'll soon be receiving. I've never done this before, to my knowledge at least, …
-
Bam file to Sanger-like chromatogram?
written by Joel Wallenius 22Hello, I'm wondering if there is a program out there that transforms a bam file (and a reference genome file) into a Sanger-like plot, e.g. …
-
Alternatives to ExpansionHunter?
written by Joel Wallenius 22Hello! My supervisor is requesting STR expansion analysis on our NGS data. I've looked into ExpansionHunter, developed by Illumina, but it only works, allegedly, on …
-
Best alignment software for mapping short DNA reads to transcriptome?
written by Joel Wallenius 22Hello! I googled but found only issues of RNA read quantification, which is fair enough but not the help I would like. I'm just curious …
-
Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way to get the correspon…
written by Joel Wallenius 22Hello! I have a list of RefSeq accession numbers of mRNA transcripts, all from homo sapiens, and would like to, for each transcript, get the …