Clint Valentine clintval

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

Keybase proof

I hereby claim:

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

To claim this, I am signing this object:

Exome Pipeline

QC Illumina flowcell, demultiplex, and QC mapped BAM

Installation · Usage · Future Improvements

Note: Build 37 coordinates.

TCGA-AB-2812   13 28608256 28608257 -  TCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAG
TCGA-AB-2825   13 28608217 28608218 -  CCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTATTCGTG
TCGA-AB-2830   13 28608242 28608243 -  ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG
TCGA-AB-2836   13 28608267 28608268 -  TTCTCTGAAATCAACGTAGAAGTACTCATTATC
TCGA-AB-2840   13 28608248 28608249 -  ATTTGAGATCATATTCAT
TCGA-AB-2844   13 28608214 28608215 -  TTACCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCT
TCGA-AB-2853   13 28608268 28608269 -  TCTCTGAAATCAACGTAG

	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

	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 *

	package com.clintval.misc

	trait CommandLineTool {
	val Executable: String
	def exec(args: String): ProcessBuilder = { new ProcessBuilder(Executable +: args: _) }
	}

	trait Testable {
	self: CommandLineTool =>
	val TestCommand: Seq[String]


	/** Implicit methods for [[Template]] objects. */
	implicit class TemplateUtil(val t: Template) {
	private def tagValue[A](records: Iterator[SamRecord], tag: String): Iterator[Option[A]] = records.map(_.get[A](tag))
	def bestEditDistanceToReference(t: Template): Option[Int] = tagValue[Int](t.allReads, SAMTag.NM.name).min
	def worstEditDistanceToReference(t: Template): Option[Int] = tagValue[Int](t.allReads, SAMTag.NM.name).max
	def bestAlignmentScore(t: Template): Option[Int] = tagValue[Int](t.allReads, SAMTag.AS.name).max
	def worstAlignmentScore(t: Template): Option[Int] = tagValue[Int](t.allReads, SAMTag.AS.name).min
	}

	from types import MethodType


	class TypeSafeAttribute(object):
	def _type_of(self, attr):
	if not self._has_attr(attr):
	raise ValueError(f'No attribute defined as annotation: {attr}')
	return self.__annotations__[attr]

	def _has_attr(self, attr):