I am developing a human variant discovery pipeline and I need some whole genome sequence human data to test it. That is, I have found, not so easy to find. Ideally it would be tumor normal but perhaps any two different WGS human fastq data would suffice as I would run it, and eventually get some vcf files with variants that I can process. Any suggestions?
•
written
by
ramiro.barrantes •
2 answers
Take a look at Genome in a Bottle https://www.nist.gov/programs-projects/genome-bottle
I recommend you look around NCBI's Sequence Read Archive. You can browse for a variety of different sequencing data sets in a very granular manner (i.e., tissue type, paired normals, sequencing platform, etc.).
I have also found this Biostars post to be particularly helpful in downloading the data locally.
Log in to answer this question.
-
Test data for benchmarking a pipeline
written by zizigolu
-
Criteria for choosing variants
written by ramiro.barrantes •
-
TCGA Germline allelic fraction distribution
written by ramiro.barrantes •
-
Gene level expression versus variant-level expression
written by ramiro.barrantes •
-
How to handle paired and unpaired reads in RNAseq pipeline
written by mohamadelian1996 •
-
Optimizing mutect/sarek for somatic substitution variant calling
written by ramiro.barrantes •
-
Different SNPs found: WGS aligned to WES
written by ramiro.barrantes •
-
Online 16S rRNA gene classification
written by mikael.lenz.strube •
-
Appropriate methodologies of comparing whole exome sequencing data between circulating tumor cells …
written by svlachavas
-
Regarding GATK pipeline
written by aj123
