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Corrected CNVnator verbose output for final vcf move. #46

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Corrected CNVnator verbose output for final vcf move. #46

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07ab8bd
Merge pull request #1 from hall-lab/master
s-boardman Sep 2, 2015
ba80c97
Corrected CNVnator verbose output.
s-boardman Sep 2, 2015
afb16f3
Window size flag and testing
s-boardman Sep 2, 2015
616f991
Merge pull request #2 from s-boardman/s-boardman-cnvnator-window-size
s-boardman Sep 21, 2015
0fbe254
OPTARGs flag for windowsize updated to w:
s-boardman Sep 21, 2015
e6938b9
Set default window size for CNVnator.
s-boardman Sep 21, 2015
3a46975
Merge pull request #4 from s-boardman/s-boardman-cnvnator-window-size
s-boardman Sep 21, 2015
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21 changes: 18 additions & 3 deletions bin/speedseq
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Original file line number Diff line number Diff line change
Expand Up @@ -1157,6 +1157,7 @@ sv options:
-x FILE BED file to exclude
-g genotype SV breakends with svtyper
-d calculate read-depth with CNVnator
-w INT CNVnator window size [100]
-A annotate the vcf with VEP
-P output LUMPY probability curves in VCF
-m INT minimum sample weight for a call [4]
Expand Down Expand Up @@ -1189,7 +1190,7 @@ global options:
MAX_SPLIT_COUNT=2
MIN_NON_OVERLAP=20

while getopts ":hB:S:D:R:o:m:r:x:T:t:AdgPkvK:" OPTION
while getopts ":hB:S:D:R:o:m:r:x:T:t:Adw:gPkvK:" OPTION
do
case "${OPTION}" in
h)
Expand Down Expand Up @@ -1235,6 +1236,9 @@ global options:
d)
READDEPTH=1
;;
w)
WINDOW_SIZE="$OPTARG"
;;
g)
GENOTYPE=1
;;
Expand Down Expand Up @@ -1342,8 +1346,20 @@ global options:
sv_usage
echo -e "Error: annotate_rd.py executable not found. Please set path in $SPEEDSEQ_DIR/speedseq.config file\n"
exit 1
elif [[ -z "$WINDOW_SIZE"]]
then
WINDOW_SIZE=100
echo -e "Using default window size: 100\n"
fi
fi

# if window size specified, check CNVnator is also specified
if [[ -n "$WINDOW_SIZE" ]] && [[ "$READDEPTH" -ne 1 ]]
then
sv_usage
echo -e "CNVnator window size passed without CNVnator; please use -d in conjunction with -w"
exit 1
fi

# check for required python modules (pysam, numpy, scipy, etc)
check_python_modules $PYTHON
Expand Down Expand Up @@ -1439,7 +1455,6 @@ global options:
if [[ "$READDEPTH" -eq 1 ]]
then
echo "Calculating read depth"
WINDOW_SIZE=100

for i in $( seq 0 $(( ${#FULL_BAM_LIST[@]}-1 )) )
do
Expand Down Expand Up @@ -1468,7 +1483,7 @@ global options:

if [[ "$VERBOSE" -eq 1 ]]
then
echo "mv $TEMP_DIR/$OUTBASE.rd.sv.vcf $TEMP_DIR/$OUTBASE.rd.sv.vcf"
echo "mv $TEMP_DIR/$OUTBASE.rd.sv.vcf $TEMP_DIR/$OUTBASE.sv.vcf"
echo "mv $TEMP_DIR/$FULL_BASE.readdepth.txt $OUTPUT.$FULL_BASE.sv.readdepth.txt"
echo "mv $TEMP_DIR/$FULL_BASE.readdepth.bed $OUTPUT.$FULL_BASE.sv.readdepth.bed"
fi
Expand Down