Hi,
Is it possible to detemine disease related variants with RNA-seq data only?
I have identify variants with RNA-seq data of disease and normal samples using GATK best pratice. What could I do to narrow down the list of variants and determine those highly related to disease?
Any advice would be appreciated.
•
written
by
wenhui •
1 answer
There are a number of third-party databases that provide information on the clinical impact of various types of short and gross germline mutations. Consider starting with HGMD, ClinVar, and/or OMIM. Information can be accessed via API or, in some cases, as databases, delimited files, or VCFs.
If you are specifically interested in somatic mutations, COSMIC or TCGA are good starting points. Be aware that somatic variant classification procedures are less characterized than those recommended for germline variant classification, especially in the clinical space. There are a number of factors to consider, e.g., tumor heterogeneity, mutational burden, algorithm performance, driver vs. passenger, etc.
Log in to answer this question.
-
GATK Mutect2
written by sk_24 •
-
Rare Disease Variant Pathway Analysis
written by The_PyPanda •
-
RNA-seq data for binary classification problem
written by botloggy •
-
How to find common alternative splicing events or novel transcripts among different batches of samp…
written by wenhui •
-
lots of transcript start at 0 and end at 1 in cufflinks output gtf file
written by wenhui •
-
RIP-Seq: Does difference in RNA pulldown conc. between Samples and Negative Control matter?
written by samantha_jeschonek
-
Why there is the same GO term in the both up- and down-regulated gene set?
written by seta
-
Practice Of Filtering Vcf Files (From Gatk)
written by newDNASeqer
-
Ways To Filter Noise From Rnaseq Data
written by Wayne
-
Snp Calling By Comparing Normal Rna-Seq Data With Disease
written by Repineme •
