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1 #!/bin/bash
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2 #input example: perc% bam comp100134_c0_seq1 28 T C
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3 #returns true if the alternative allele occurs in >= than perc (%) cases
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4
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5 perc=$1; bam=$2; contig=$3; position=$4; ref=$5; alt=$6;
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6
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7 echo contig $contig position $position ref $ref alt $alt >>kontrola;
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8
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9 depth=0;
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10
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11 perl ${LINKYX_PATH}/scripts/bam_analysis.pl $bam reference.fasta $contig $position; #writes to mpileup;
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12 pro_hits=`grep -w "$alt" mpileup | cut -f2 -d":"`;
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13
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14 if [ -z "$pro_hits" ]; then
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15 hits=0;
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16 else
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17 hits=$pro_hits;
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18 fi
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19
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20 depth=`grep -w "DEPTH" mpileup | cut -f2 -d":"`;
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21
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22 echo "hits: " $hits " depth: " $depth >>kontrola;
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23
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24 if [[ $depth -eq $zero ]]; then
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25 echo "0";
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26 exit;
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27 fi
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28
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29 if [ $depth -lt 5 ]; then
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30 #depth <=4
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31 if [ $hits -gt 0 ]; then
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32 echo "1"; #in this depth, none of variants can be tolerated
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33 else
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34 echo "0"; #ok
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35 fi
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36 else
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37 if [ $depth -lt 25 ]; then
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38 #depth 5..24
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39 if [ $hits -gt 1 ]; then
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40 echo "1"; #in this depth, one variant can be tolerated
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41 else
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42 echo "0"; #ok
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43 fi
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44 else
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45 #depth >=25
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46 hits=$[hits*100];
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47 percentage=`echo "scale=3; $hits/$depth" | bc`;
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48
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49 if (( $(echo "$perc < $percentage"|bc -l) )); then
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50 echo "1"; #too much of WRONG variants
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51 else
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52 echo "0"; #in tolerance
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53 fi
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54 fi
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55 fi
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56
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57
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