Hack a BAM into LUMPY parts

gistfile1.sh

BAM=your.bam
OUT_DIR=what_lumpy_needs

LUMPY_HOME=$HOME/src/lumpy-sv
SAMBAMBA=$HOME/bin/sambamba
SAMBLASTER=$HOME/bin/samblaster
SAMTOBAM="$SAMBAMBA view -S -f bam -l 0"
SAMSORT="$SAMBAMBA sort -m 1G --tmpdir "
PAIREND_DISTRO=$LUMPY_HOME/scripts/pairend_distro.py
BAMGROUPREADS=$LUMPY_HOME/scripts/bamkit/bamgroupreads.py
MAX_SPLIT_COUNT=2
MIN_NON_OVERLAP=20

BAM_BASE=`basename $BAM .bam`
OUTPUT=`basename $BAM`.vcf
OUTBASE=`basename "$OUTPUT"`

# make pipes
TEMP_DIR=$OUT_DIR/$BAM_BASE
mkdir -p $TEMP_DIR/spl $TEMP_DIR/disc
mkfifo $TEMP_DIR/spl_pipe
mkfifo $TEMP_DIR/disc_pipe

READ_LENGTH=`$SAMBAMBA view $BAM | head -n 10000 | awk 'BEGIN { MAX_LEN=0 } { LEN=length($10); if (LEN>MAX_LEN) MAX_LEN=LEN } END { print MAX_LEN }'`

$PYTHON $BAMGROUPREADS \
    --fix_flags \
    -i $BAM \
| $SAMBLASTER \
    --acceptDupMarks \
    --excludeDups \
    --addMateTags \
    --maxSplitCount $MAX_SPLIT_COUNT \
    --minNonOverlap $MIN_NON_OVERLAP \
    --splitterFile $TEMP_DIR/spl_pipe \
    --discordantFile $TEMP_DIR/disc_pipe \
| $SAMBAMBA view -S /dev/stdin \
| awk '{if (NR<=1000000)
            print > "/dev/stdout";
        else
            print > "/dev/null" }' \
| $PYTHON $PAIREND_DISTRO \
    -r $READ_LENGTH \
    -X 4 \
    -N 1000000 \
    -o ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).x4.histo \
> ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats &

$SAMTOBAM $TEMP_DIR/spl_pipe \
| $SAMSORT $TEMP_DIR/spl \
    -o $TEMP_DIR/$OUTBASE.sample$(($i+1)).lib$(($j+1)).splitters.bam \
    /dev/stdin &

$SAMTOBAM $TEMP_DIR/disc_pipe \
| $SAMSORT $TEMP_DIR/disc \
    -o $TEMP_DIR/$OUTBASE.sample$(($i+1)).lib$(($j+1)).discordants.bam \
    /dev/stdin

wait

rm $TEMP_DIR/spl_pipe
rm $TEMP_DIR/disc_pipe
rmdir $TEMP_DIR/spl
rmdir $TEMP_DIR/disc