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comparison snpEff_2_1a/scripts/sift2vcf.sh @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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1 #!/bin/sh -e
2
3 SQLITE=$HOME/tools/sqlite3
4 SQLITE=sqlite3
5 OUT_FILE="sift.txt"
6 OUT_SORT_FILE="sift.sort.txt"
7 OUT_VCF="sift.vcf"
8
9 # Download files
10 for f in Human_CHR1.sqlite.gz Human_CHR10.sqlite.gz Human_CHR11.sqlite.gz Human_CHR12.sqlite.gz Human_CHR13.sqlite.gz Human_CHR14.sqlite.gz Human_CHR15.sqlite.gz Human_CHR16.sqlite.gz Human_CHR17.sqlite.gz Human_CHR18.sqlite.gz Human_CHR19.sqlite.gz Human_CHR2.sqlite.gz Human_CHR20.sqlite.gz Human_CHR21.sqlite.gz Human_CHR22.sqlite.gz Human_CHR3.sqlite.gz Human_CHR4.sqlite.gz Human_CHR5.sqlite.gz Human_CHR6.sqlite.gz Human_CHR7.sqlite.gz Human_CHR8.sqlite.gz Human_CHR9.sqlite.gz Human_CHRX.sqlite.gz Human_CHRY.sqlite.gz Human_Supp.sqlite.gz Human_enst.sqlite.gz
11 do
12 url=ftp://ftp.jcvi.org/pub/data/sift/Human_db_37_ensembl_63/$f
13 echo Getting file $url
14 #wget $url
15 done
16
17 # Unzip files
18 for f in Human_CHR*.sqlite.gz
19 do
20 echo Decompressing file $f
21 #gunzip $f
22 done
23
24 # Dumping data
25 rm -f $OUT_FILE
26 for f in Human_CHR*.sqlite
27 do
28 echo Dumping Database $f to $OUT_FILE
29
30 TABLES=`$SQLITE $f ".tables" | tr "\n" "\t"`
31 for t in $TABLES
32 do
33 echo " Dumping Table $t"
34
35 $SQLITE $f "select CHR, COORD1, NT1, NT2, SCORE, MEDIAN, SEQS_REP from $t where SCORE != '' AND NT1 != NT2;" \
36 | tr "|" "\t" \
37 | sed "s/^chr//" \
38 >> $OUT_FILE
39 done
40 done
41
42 echo Sorting file
43 sort -k 1 -n -k 2 -n -o $OUT_SORT_FILE $OUT_FILE
44
45 echo Creating VCF
46 cat $OUT_SORT_FILE | sift2vcf.pl > $OUT_VCF
47