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13
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1 #!/bin/sh
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2 #$ -V
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3 #$ -cwd
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4 #$ -q 1-day
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5 #$ -m ae
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6 #$ -M hart.steven@mayo.edu
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7 #$ -l h_vmem=1G
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8 #$ -l h_stack=10M
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9 BAM=$1
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10 TARGET_BED=$2
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11 SAMPLE_NUMBER=$3
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12
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13 #cat $HEADER > out.${SAMPLE_NUMBER}.sam
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14 samtools view -L $TARGET_BED $BAM|
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15 perl -ane '
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16 next if ($F[10]=~/#/);
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17 $minSize=1000;
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18 if( $F[1] & 8 || $F[1] & 4 || $F[8] == 0 || abs($F[8]) > $minSize || $F[5] =~/S/){
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19 $rName=join("","@",@F[0]);
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20 print join ("\n",$rName,$F[9],"+",@F[10])."\n";
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21 };
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22 ' >> out.${SAMPLE_NUMBER}.fq
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23 echo "Done with $BAM `date`"
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