|
0
|
1 #!/bin/bash
|
|
|
2 set -e;
|
|
|
3
|
|
|
4 #read config variables
|
|
|
5 echo "Reading config...." >&2
|
|
|
6 #echo `ls -l`
|
|
|
7 computer_name=`hostname`;
|
|
|
8 if [ $computer_name == "misa" ]; then
|
|
|
9 #local_computer
|
|
|
10 source config_devel;
|
|
|
11 else
|
|
|
12 #metacentrum machine
|
|
|
13 source config_meta;
|
|
|
14 fi
|
|
|
15
|
|
|
16 #files needed: reference_male.fasta $reads_1 $reads_2
|
|
|
17
|
|
|
18 reference=$1;
|
|
|
19 reads_1="input/$2"; echo "reads_1: " $reads_1;
|
|
|
20 reads_2="input/$3"; echo "reads_2: " $reads_2;
|
|
|
21 name=$4;
|
|
|
22 fragments=$5;
|
|
|
23
|
|
|
24 #INDEXING FILES
|
|
|
25
|
|
|
26 if [ -e "references/reference_male.dict" ];
|
|
|
27 then
|
|
|
28 echo "Reference exists. Not being created again.";
|
|
|
29 else
|
|
|
30 echo "seconds of run: $SECONDS";
|
|
|
31 java -jar $CreateSequenceDictionary R=$reference O=references/reference_male.dict >mlogfile 2>>errlogfile;
|
|
|
32 echo "0/9 INDEXING FILES successful";
|
|
|
33 echo "seconds of run: $SECONDS";
|
|
|
34 fi
|
|
|
35
|
|
|
36 if [ -e "references/reference_male.fai" ];
|
|
|
37 then
|
|
|
38 echo "Samtools reference exists. Not being created again.";
|
|
|
39 else
|
|
|
40 echo "seconds of run: $SECONDS";
|
|
|
41 echo "reference:"$reference;
|
|
|
42 samtools faidx $reference 2>>errlogfile;
|
|
|
43 echo "0/9 INDEXING FILES successful";
|
|
|
44 echo "seconds of run: $SECONDS";
|
|
|
45 fi
|
|
|
46
|
|
|
47 #1 MAPPING WITH BWA
|
|
|
48 bwa index $reference >>mlogfile 2>>errlogfile;
|
|
|
49
|
|
|
50 #differs based on the fact whether reads are single or paired-end
|
|
|
51 bwa aln -t 2 $reference $reads_1 > bam/aln_sa1_${name}_male.sai & 2>>errlogfile;
|
|
|
52 wait;
|
|
|
53
|
|
|
54 if [[ $fragments =~ (single) ]]; then
|
|
|
55 #single end reads
|
|
|
56 bwa samse $reference bam/aln_sa1_${name}_male.sai $reads_1 > bam/aln_${name}_male.sam 2>>errlogfile;
|
|
|
57 echo "bwa samse $reference bam/aln_sa1_${name}_male.sai $reads_1 > bam/aln_${name}_male.sam 2>>errlogfile";
|
|
|
58 else
|
|
|
59 #pair-end reads
|
|
|
60 bwa aln -t 2 $reference $reads_2 > bam/aln_sa2_${name}_male.sai & 2>>errlogfile;
|
|
|
61 echo "bwa aln -t 2 $reference $reads_2 > bam/aln_sa2_${name}_male.sai & 2>>errlogfile";
|
|
|
62 wait;
|
|
|
63 bwa sampe $reference bam/aln_sa1_${name}_male.sai bam/aln_sa2_${name}_male.sai $reads_1 $reads_2 > bam/aln_${name}_male.sam 2>>errlogfile;
|
|
|
64 echo "bwa sampe $reference bam/aln_sa1_${name}_male.sai bam/aln_sa2_${name}_male.sai $reads_1 $reads_2 > bam/aln_${name}_male.sam 2>>errlogfile";
|
|
|
65 fi
|
|
|
66
|
|
|
67 wait;
|
|
|
68 rm -f bam/aln_sa1_${name}_male.sai bam/aln_sa2_${name}_male.sai
|
|
|
69
|
|
|
70
|
|
|
71 echo "1/6 MAPPING WITH BWA successful";
|
|
|
72 echo "seconds of run: $SECONDS";
|
|
|
73
|
|
|
74 #2 CLEANING FILES - adjust MAPQ scores
|
|
|
75 echo "$SECONDS";
|
|
|
76 java -jar $CleanSam I=bam/aln_${name}_male.sam O=bam/aln_cleaned_${name}_male.sam 2>>/dev/null;
|
|
|
77 echo "2/6 CLEANING FILES - adjust MAPQ scores successful";
|
|
|
78 echo "seconds of run: $SECONDS";
|
|
|
79 wait
|
|
|
80
|
|
|
81 #3 CONVERTING TO BAM FILE
|
|
|
82 samtools view -bS bam/aln_cleaned_${name}_male.sam > bam/aln_cleaned_${name}_male.bam 2>>errlogfile;
|
|
|
83 echo "3/6 CONVERTING TO BAM FILE successful";
|
|
|
84 echo "seconds of run: $SECONDS";
|
|
|
85 wait
|
|
|
86
|
|
|
87 #4 SORTING BAM FILE
|
|
|
88 samtools sort bam/aln_cleaned_${name}_male.bam bam/aln_cleaned_sorted_${name}_male >mlogfile 2>>errlogfile;
|
|
|
89 echo "4/6 SORTING BAM FILE successful";
|
|
|
90 echo "seconds of run: $SECONDS";
|
|
|
91 wait;
|
|
|
92
|
|
|
93 #5 REMOVING DUPLICATES
|
|
|
94 java -jar $MarkDuplicates INPUT=bam/aln_cleaned_sorted_${name}_male.bam OUTPUT=bam/aln_cleaned_sorted_deduplicated_${name}_male.bam METRICS_FILE=picard_info.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 2>>/dev/null;
|
|
|
95 echo "5/6 REMOVING DUPLICATES successful";
|
|
|
96 echo "seconds of run: $SECONDS";
|
|
|
97 wait;
|
|
|
98
|
|
|
99 #9 REMOVING FILES
|
|
|
100 rm -f bam/aln_${name}_male.sam bam/aln_cleaned_${name}_male.sam bam/aln_cleaned_${name}_male.bam bam/aln_cleaned_sorted_${name}_male.bam >>mlogfile 2>>errlogfile;
|
|
|
101 echo "6/6 REMOVING FILES successful";
|
|
|
102 echo "seconds of run: $SECONDS";
|
|
|
103 echo "DONE";
|
|
|
104
|
