allgenesconsidered

library("SNPRelate")
snpgdsVCF2GDS(vcf.fn = "~/Desktop/dom_neg_genes_chr11_only/domneg_filtered_variants.vcf", out.fn = "~/Desktop/my.gds")

snpgdsSummary("~/Desktop/my.gds")

genofile <- openfn.gds("~/Desktop/my.gds")


ibs.hc <- snpgdsHCluster(snpgdsIBS(genofile, num.thread=2))
rv <- snpgdsCutTree(ibs.hc)

allgenesconsidered

## Generate combine files
# freq_1 <- read.delim('filter_for_common/dat_vc/BEST1_very_common.tsv', header = T, stringsAsFactors = F)
# freq_1$gene <- 'BEST1'
# freq_2 <- read.delim('filter_for_common/dat_vc/HSPB1_very_common.tsv', header = T, stringsAsFactors = F)
# freq_2$gene <- 'HSPB1'
# freq_3 <- read.delim('filter_for_common/dat_vc/MFN2_very_common.tsv', header = T, stringsAsFactors = F)
# freq_3$gene <- 'MFN2'
# freq_4 <- read.delim('filter_for_common/dat_vc/NEFL_very_common.tsv', header = T, stringsAsFactors = F)
# freq_4$gene <- 'NEFL'
# 

allgenesconsidered

#!/bin/bash

cd /data/home/molvera/res

wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
wget -c	ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/hapmap_3.3.hg38.vcf.gz
wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/hapmap_3.3.hg38.vcf.gz.tbi

allgenesconsidered

#!/bin/bash

PI="/data/home/molvera/opt"
cd /data/home/molvera/wgs-patient-data

for SAMPLE in "MN_P1_S5" "NF_P1_S1" "BT_P1_S2"
do

java -Xmx10g -jar $PI/picard.jar SortSam\
 INPUT=./sam/$SAMPLE.sam\

allgenesconsidered

#!/bin/bash

cd /data/home/molvera/wgs-patient-data # Change the directory to my project directory

REF=/data/home/molvera/opt/hg38/Homo_sapiens_assembly38.fasta # Create a variable assigning REF to the absolute location 
# of my .fasta reference file. 

bwa index $REF # The first part of BWA, which indexes your reference file. You only need to do this once per fasta reference.

for samp in "BT_P1_S2" "BT_P3_S9" "BT_P6_S7" "BT_P7_S6" "BT_P8_S3" # For loop through my 5 samples. 

allgenesconsidered

<% @todos.each do |todo| %>
  <li>
    YOUR CODE HERE
  </li>
<% end %>

allgenesconsidered

<div class="card">
  <h2>Edit this todo...</h2>

  <form action="#">
    <input class="text-input" name="description" type="text" value="<%= @todo.description %>">
    <input class="text-input" name="pomodoro_estimate" type="number" value="<%= @todo.pomodoro_estimate %>">
    <input class="button add-new-todo-button" type="submit" value="Edit todo">
    <a href="/todo/index" class="simple-link">Go back...</a>
  </form>
</div>

allgenesconsidered

<h2>Add a new todo...</h2>

<form action="#">
  <input class="text-input" id="new-todo-description" name="description" type="text" placeholder="Add a new todo...">
  <input class="text-input" id="new-pomodoro-estimate" name="pomodoro_estimate" type="number" placeholder="Pomodoro estimate...">
  <input class="button" id="add-new-todo-button" type="submit" value="Add todo">
</form>

allgenesconsidered

<li>
  <input type="checkbox" name=""/>
  <a href="show/1">Make the curriculum</a>
  <span class="pomodoro-estimate small-pomodoro-estimate">4 Pomodoros</span>
</li>

allgenesconsidered

def show
  todo_id = params[:id]

  if todo_id == '1'
    @todo_description = "Make the curriculum"
    @todo_pomodoro_estimate = 4

  elsif todo_id == '2'
    @todo_description = "Buy workshop supplies"
    @todo_pomodoro_estimate = 3