1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
|
#!/bin/bash
if [ -z $5 ]
then
echo "$0 <min_mapping_threshold> <back_distance> <tt> <read len> <pe bam> <e>"
exit
fi
MIN_MAP_T=$1
BACK=$2
TT=$3
READ_LENGTH=$4
PE_BAM=$5
E=$6
Z=4
WEIGHT=4
OUT_DIR=`dirname $PE_BAM`
OUT_FILE=`basename $PE_BAM .bam`
MEAN_STDEV=`samtools view $PE_BAM \
| ../scripts/pairend_distro.py \
-r $READ_LENGTH \
-X $Z \
-N 10000 \
-o $OUT_DIR/$OUT_FILE.histo`
MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
../bin/lumpy \
-b \
-mw $WEIGHT \
-tt $TT \
-pe \
bam_file:$PE_BAM,histo_file:$OUT_DIR/$OUT_FILE.histo,mean:$MEAN,stdev:$STDEV,read_length:$READ_LENGTH,min_non_overlap:$READ_LENGTH,discordant_z:4,back_distance:$BACK,weight:1,id:1,min_mapping_threshold:$MIN_MAP_T\
> $OUT_DIR/$OUT_FILE.pe.bedpe
if [ `command -v bedtools` ]
then
EX=`cat $E | wc -l`
O=`cat $OUT_DIR/$OUT_FILE.pe.bedpe | wc -l`
C=`bedtools pairtopair \
-a $E \
-b $OUT_DIR/$OUT_FILE.pe.bedpe \
-type both -is -slop 3 \
| cut -f7 | sort -u | wc -l`
I=`bedtools pairtopair \
-b $E \
-a $OUT_DIR/$OUT_FILE.pe.bedpe \
-type notboth -is -slop 3 \
| cut -f 7 | sort -u | wc -l`
echo -e "Simulated:$EX\tPredicted:$O\tTrue:$C\tFalse:$I"
else
echo "Install bedtools to compare result to known deletions"
fi
|
