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|
#!/bin/bash
if [ -z $5 ]
then
echo "$0 <min_mapping_threshold> <back_distance> <tt> <read len> <rl bam> <e>"
exit
fi
MIN_MAP_T=$1
BACK=$2
TT=$3
READ_LENGTH=$4
SR_BAM=$5
E=$6
Z=4
WEIGHT=4
OUT_DIR=`dirname $SR_BAM`
OUT_FILE=`basename $SR_BAM .bam`
../bin/lumpy \
-b \
-mw $WEIGHT \
-tt $TT \
-sr \
bam_file:$SR_BAM,back_distance:$2,weight:1,id:1,min_mapping_threshold:$1 \
> $OUT_DIR/$OUT_FILE.sr.bedpe
if [ `command -v bedtools` ]
then
EX=`cat $E | wc -l`
O=`cat $OUT_DIR/$OUT_FILE.sr.bedpe | wc -l`
C=`bedtools pairtopair \
-a $E \
-b $OUT_DIR/$OUT_FILE.sr.bedpe \
-type both -is -slop 3 \
| cut -f7 | sort -u | wc -l`
I=`bedtools pairtopair \
-b $E \
-a $OUT_DIR/$OUT_FILE.sr.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
|
