Shawn Rynearson srynobio

gantry | ˈɡantrē |

Introduction

Run Singularity containers a bit easier! Allows users the ablility to:

List all currently available singularity images.
Run single or multiple commands through a singularity container.

UCGD-Pipeline VAR project setup.

This is a walkthrough of the UCGD Pipeline simplified project setup.

Step one:

Complete project setup.

└── UCGD
    └── GRCh38
        ├── Data
        │   └── PolishedCrams
        └── VCF
            └── GVCFs
    └── GRCh37
        ├── Data
 │ └── PolishedCrams

Run below as script (after configuring the bash variables)

First step subsets VCF to trio for Slivar (discard sites where family is all homref)

Second step subsets the trio VCF to individuals for Fabric upload (keep homref sites)

Notes:

Reheader VCF to correct bug in Sentieon where AD format in header is "." instead of "R" This is important for both decomposing multi-allelic sites and subsetting by sample. This step will no

UCGD Reprocessed Phase3 WGS Overview.

This is an overview of and where to find data for the Phase3 WGS 1000Genome data (3,202 individuals). This data was downloaded from S3, and realigned (GRCh38) using the standard UCGD Pipeline.

Data can be accessed here:

redwood servers.
Mosaic (To be populated)

CRAM Files

I've tried to add notes along to help get you on the right path:

params.fasta = "/kbod2/ReferenceGenomes/GRCh37/human_g1k_v37_decoy_phix.fasta"
params.fai = "/kbod2/ReferenceGenomes/GRCh37/human_g1k_v37_decoy_phix.fai"
params.dbsnp = "/ybod2/cavery/Resources/dbsnp_146.hg38.vcf"
params.reference_mills_1000G = "/ybod2/cavery/Resources/Mills_and_1000G_gold_standard.indels.hg38.vcf"
params.reference_1000G_HighConfSNP = "/ybod2/cavery/Resources/1000G_phase1.snps.high_confidence.hg38.vcf"
params.results = "/ybod2/cavery/gatk_nextflow_files/"

	$> nslookup sequenceontology.org
	Server: 172.20.120.20
	Address: 172.20.120.20#53

	Non-authoritative answer:
	Name: sequenceontology.org
	Address: 216.21.224.198

	I called the DNS company yesterday and asked them to update the IP of sequenceontology.org to 155.101.145.21 but I believe they reverted
	it back to 216.21.224.198 based on the nslookup.

	## I've testing adding sample as a name and as a path to a file.
	## I have ran this code and `response.ok` returns true, but the project has no change at the sample level
	## https://mosaic-staging.chpc.utah.edu/#/projects/459/

	def post_sample(mosaic_meta, sample, project_id):
	path = "{}/projects/{}/samples"
	url = path.format(mosaic_meta['url'], project_id)

	headers = {
	'Authorization' : mosaic_meta['authorization'],

	### ------------------------------------------------------------------- ##

	def post_sample(mosaic_meta, sample, project_id, data_file):
	path = "{}/projects/{}/samples"
	url = path.format(mosaic_meta['url'], project_id)

	headers = {
	'Authorization' : mosaic_meta['authorization'],
	}
	data = {