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ClinVar

This directory contains:

• ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) dataset reports, and ClinVar development documents
• documents related to the NCBI collaboration with ClinGen (http://www.clinicalgenome.org/)
• ftp://ftp.ncbi.nih.gov/pub/clinvar/ClinGen/ExpertPanelRequestForm.docx - how to apply for expert panel status
• data common to ClinVar and GTR
• ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms - terminology used by both GTR and ClinVar.

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#!/bin/bash
samtools=`which samtools`
bn=$(basename $1 .bam)

echo processing $bn
$samtools view -h -b -f99  $1 > $bn.flag99.bam
$samtools view -h -b -f147 $1 > $bn.flag147.bam
$samtools view -h -b -f163 $1 > $bn.flag163.bam
$samtools view -h -b -f83  $1 > $bn.flag83.bam

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# 0 is too far from ` ;)
set -g base-index 1

# Automatically set window title
set-window-option -g automatic-rename on
set-option -g set-titles on

#set -g default-terminal screen-256color
set -g status-keys vi
set -g history-limit 10000

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tmux cheat sheet

(C-x means ctrl+x, M-x means alt+x)

Prefix key

The default prefix is C-b. If you (or your muscle memory) prefer C-a, you need to add this to ~/.tmux.conf:

remap prefix to Control + a

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#!/bin/bash

# Wrapper to run interactive job on helix hpc.
# @sbamin | helix

# usage
show_help() {
cat << EOF

Start interactive job on Helix: Only one job is allowed at a time.

ipstone

Setting up Emacs daemon on OS X

Tired of waiting for emacs to start on OS X? This step by step guide will teach you how to install the latest version of emacs and configure it to start in the background (daemon mode) and use emacsclient as your main editor.

Install Cocoa Emacs

Download the latest pretest version of [Emacs for Mac OS X]: http://emacsformacosx.com/builds

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FFmpeg cheat sheet

A list of useful commands for the ffmpeg command line tool.

Download FFmpeg: https://www.ffmpeg.org/download.html

Full documentation: https://www.ffmpeg.org/ffmpeg.html

Basic conversion