1 | #Set parameters and values |
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2 | GSAPUBFTP_PATH="bundle/2.8/b37" |
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3 | ROOT="/volume/" |
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4 | RESDIR="$ROOT/resources/b37/" |
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5 | TMPDIR="$ROOT/tmp" |
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6 | BWAVERSION="0.7.12-goolf-1.7.20" |
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7 | |
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8 | |
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9 | ###Create tmp directory and cd to it |
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10 | mkdir -p $TMPDIR |
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11 | cd $TMPDIR |
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12 | |
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13 | |
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14 | ###wget resources |
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15 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/human_g1k_v37.dict.gz |
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16 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/human_g1k_v37.dict.gz.md5 |
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17 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/human_g1k_v37.fasta.gz |
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18 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/human_g1k_v37.fasta.gz.md5 |
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19 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/human_g1k_v37.fasta.fai.gz |
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20 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/human_g1k_v37.fasta.fai.gz.md5 |
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21 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/Mills_and_1000G_gold_standard.indels.b37.vcf.gz |
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22 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 |
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23 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz |
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24 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5 |
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25 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.vcf.gz |
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26 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.vcf.gz.md5 |
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27 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.vcf.idx.gz |
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28 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.vcf.idx.gz.md5 |
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29 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.excluding_sites_after_129.vcf.gz |
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30 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.excluding_sites_after_129.vcf.gz.md5 |
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31 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.excluding_sites_after_129.vcf.idx.gz |
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32 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/dbsnp_138.b37.excluding_sites_after_129.vcf.idx.gz.md5 |
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33 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/1000G_phase1.indels.b37.vcf.gz |
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34 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/1000G_phase1.indels.b37.vcf.gz.md5 |
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35 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/1000G_phase1.indels.b37.vcf.idx.gz |
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36 | wget ftp://gsapubftp-anonymous@ftp.broadinstitute.org//$GSAPUBFTP_PATH/1000G_phase1.indels.b37.vcf.idx.gz.md5 |
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37 | wget https://molgenis26.target.rug.nl/downloads/intervals/testKit1_baits_b37_human_g1k_v37.bed |
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38 | wget https://molgenis26.target.rug.nl/downloads/intervals/testKit1_baits_b37_human_g1k_v37.interval_list |
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39 | wget https://molgenis26.target.rug.nl/downloads/intervals/testKit1_exons_b37_human_g1k_v37.bed |
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40 | wget https://molgenis26.target.rug.nl/downloads/intervals/testKit1_exons_b37_human_g1k_v37.interval_list |
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41 | wget https://molgenis26.target.rug.nl/downloads/intervals/1000G_phase1.indels_Mills_and_1000G_gold_standard.indels.b37.human_g1k_v37.chr1.intervals |
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42 | |
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43 | |
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44 | ###Generate correct md5sum files |
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45 | for i in $( ls *.md5 ); |
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46 | do |
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47 | echo "Generating correct md5sum file for $i"; |
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48 | |
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49 | SUM=`awk '{print $1}' $i`; |
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50 | FILENAME=`cat $i | xargs -0 basename`; |
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51 | |
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52 | echo -e "$SUM $FILENAME" > $i.proper.md5; |
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53 | |
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54 | rm $i; |
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55 | |
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56 | done |
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57 | |
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58 | |
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59 | ###Check md5sums generated files |
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60 | for i in $( ls *.proper.md5 ); |
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61 | do |
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62 | echo "Checking md5sum for file $i"; |
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63 | |
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64 | md5sum -c $i; |
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65 | |
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66 | done |
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67 | |
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68 | |
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69 | ###Unzip all *.gz files |
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70 | for i in $( ls *.gz ); |
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71 | do |
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72 | echo "Gunzipping file $i"; |
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73 | |
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74 | gunzip $i; |
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75 | |
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76 | done |
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77 | |
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78 | |
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79 | ###Index reference genome using BWA |
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80 | module use /srv/molgenis/.local/easybuild/modules/all/ |
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81 | module avail |
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82 | module load BWA/$BWAVERSION |
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83 | |
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84 | bwa index -p human_g1k_v37.fasta -a bwtsw human_g1k_v37.fasta |
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85 | |
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86 | |
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87 | ###Create folder structure for resources |
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88 | mkdir -p $RESDIR/indices/ |
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89 | mkdir -p $RESDIR/intervals/ |
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90 | mkdir -p $RESDIR/snp/dbSNP/ |
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91 | mkdir -p $RESDIR/snp/1000G/ |
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92 | mkdir -p $RESDIR/sv/1000G |
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93 | |
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94 | |
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95 | ###Move all resources to correct folder |
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96 | mv human_g1k_v37.dict $RESDIR/indices/ |
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97 | mv human_g1k_v37.fasta $RESDIR/indices/ |
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98 | mv human_g1k_v37.fasta.amb $RESDIR/indices/ |
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99 | mv human_g1k_v37.fasta.ann $RESDIR/indices/ |
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100 | mv human_g1k_v37.fasta.bwt $RESDIR/indices/ |
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101 | mv human_g1k_v37.fasta.pac $RESDIR/indices/ |
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102 | mv human_g1k_v37.fasta.sa $RESDIR/indices/ |
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103 | mv human_g1k_v37.fasta.fai $RESDIR/indices/ |
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104 | mv Mills_and_1000G_gold_standard.indels.b37.vcf $RESDIR/sv/1000G |
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105 | mv Mills_and_1000G_gold_standard.indels.b37.vcf.idx $RESDIR/sv/1000G |
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106 | mv dbsnp_138.b37.vcf $RESDIR/snp/dbSNP/ |
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107 | mv dbsnp_138.b37.vcf.idx $RESDIR/snp/dbSNP/ |
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108 | mv dbsnp_138.b37.excluding_sites_after_129.vcf $RESDIR/snp/dbSNP/ |
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109 | mv dbsnp_138.b37.excluding_sites_after_129.vcf.idx $RESDIR/snp/dbSNP/ |
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110 | mv 1000G_phase1.indels.b37.vcf $RESDIR/sv/1000G |
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111 | mv 1000G_phase1.indels.b37.vcf.idx $RESDIR/sv/1000G |
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112 | mv testKit1_baits_b37_human_g1k_v37.bed $RESDIR/intervals/ |
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113 | mv testKit1_baits_b37_human_g1k_v37.interval_list $RESDIR/intervals/ |
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114 | mv testKit1_exons_b37_human_g1k_v37.bed $RESDIR/intervals/ |
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115 | mv testKit1_exons_b37_human_g1k_v37.interval_list $RESDIR/intervals/ |
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116 | mv 1000G_phase1.indels_Mills_and_1000G_gold_standard.indels.b37.human_g1k_v37.chr1.intervals $RESDIR/intervals/ |
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117 | |
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118 | ###Remove temporary folder |
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119 | rm -r $TMPDIR |
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