Clint Valentine clintval

Exome Pipeline

QC Illumina flowcell, demultiplex, and QC mapped BAM

Installation · Usage · Future Improvements

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I am clintval on github.
I am clintval (https://keybase.io/clintval) on keybase.
I have a public key ASA1U0QRFP5NAtESP-6ztuMfcyXE23LNCGe9r7Vlb71nRgo

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INFO Fields

Key	Definition
SAMPLE	Sample name
TYPE	Variant Type: SNV Insertion Deletion Complex
DP	Total depth
End	Chromosome end position
VD	Variant depth
AF	Allele frequency

GenBank Accession Number Reference Sheet:

The International Nucleotide Sequence Database Collaboration (INSDC) consists of the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL) and GenBank at NCBI. As part of the Collaboration, all three organizations accept new sequence submissions and share sequence data among the three databases. To facilitate the exchange of data, each member of the collaboration is assigned certain accession prefixes. In addition to the accession number, GenBank records also have a GI number. The GI number is simply a series of digits assigned consecutively to sequences submitted to NCBI.

Format of GenBank accession numbers:

Fooled by the timezone you live in?

EDT - implicit

❯ aws s3 ls s3://example-ngs-data/30-415555663/ | head -n1
2020-10-14 17:57:17 24784494053 sample-1_S21_L003_R1_001.fastq.gz

PDT - explicit

	from collections import defaultdict

	import matplotlib.pyplot as plt
	import numpy as np
	import vcf

	from palettable.colorbrewer.qualitative import Paired_12
	from scipy.stats import gaussian_kde

	from vcf_figures.helpers import *

	Name,Slack Call Sign,Location,Interests,Skills (General),Preferred Language,Programming Languages,Education Background,Github Username,Preferred group within collab
	Mark van der Sman,mvdsman,"Leiden, The Netherlands","Visualisation, genomics, pattern recognition/ML, statistical analysis, phylogenetics/evolution (and many more)","Visualisation, genomics, web development, some transcriptomics and some Machine Learning/Natural Computing. Biologist going for MSc BI",R,"Most experienced in R/RShiny, decent in Python and HTML/CSS/Markdown, basics in C++, PHP, SQL. Flaming hatred towards Matlab","B.Sc. Biology + minor Data Science, going for M.Sc. Bioinformatics",MvdSman,Visualisation
	Anthony Fejes,apfejes,"Bay Area, California","Visualization, transcriptomics, epigenomics, genomics,","Biologist, biochemist, programmer, entrepreneur",Python,"Python, C, SQL/No-SQL, Java, etc. (Anything except R, Javascript)","B.Sc. Biochemitry
	B.I.S.
	M.Sc. Microbiology and Immunology
	PhD. Bioinformatics",apfejes,
	Dimitrios - Georgios

	# Requires the STAR executable to be at:
	# /pipeline/packages/star
	#

	# Overhang is set to the read length (template cycles) of 142 - 1:
	#
	OVERHANG=141

	git clone \
	https://github.com/dpryan79/ChromosomeMappings.git \

	# After a `pip install sample-sheet pendant`

	from sample_sheet import SampleSheet
	from pendant.aws.s3 import S3Uri

	def s3_validate_sample_sheet(path):
	for sample in SampleSheet(path):
	left = S3Uri(sample.PathToFastq1)
	right = S3Uri(sample.PathToFastq2)
	assert left.object_exists()

	object SampleUtil {

	/** Join all of the data across a collection of samples. All fields will be joined on the delimiter `";"`. Regardless
	* of the lanes the libraries were sequenced on, the resulting sample will have the lanes field cleared to [[None]].
	* The merged sample will have its ordinal set to zero.
	*
	* @throws IllegalArgumentException when there are no libraries to merge
	* @throws IllegalArgumentException when trying to join samples with different sample names
	*/
	def merge(samples: Seq[Sample]): Sample = {