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bwa-gatk.json
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{
"define":
{
"SPLITS":10,
"SLICES":10,
"GRANULARITY":40000,
"BWA":"./bwa",
"REF":"oak2.fa",
"REF_INDEX":
[
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac"
],
"SPLIT_ALIGN":"gatk_split_align",
"SAMTOOLS":"./samtools",
"PICARD":"picard.jar",
"GATK":"GenomeAnalysisTK.jar",
"ORGANISMS":
[
"10001",
"10012",
"10024",
"10034",
"10045",
"10062",
"10081",
"10002",
"10015",
"10025",
"10036",
"10046",
"10072",
"10082",
"10003",
"10016",
"10026",
"10037",
"10048",
"10074",
"10004",
"10017",
"10027",
"10039",
"10049",
"10075",
"10005",
"10018",
"10028",
"10040",
"10050",
"10076",
"10006",
"10019",
"10029",
"10041",
"10051",
"10077",
"10007",
"10021",
"10030",
"10042",
"10060",
"10078",
"10009",
"10023",
"10031",
"10044",
"10061",
"10079"
]
},
"rules":
[
{
"command":"./bwa aln oak2.fa SM10001.fq > SM10001.sai 2> SM10001.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10001.fq"
],
"outputs":
[
"SM10001.sai",
"SM10001.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10012.fq > SM10012.sai 2> SM10012.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10012.fq"
],
"outputs":
[
"SM10012.sai",
"SM10012.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10024.fq > SM10024.sai 2> SM10024.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10024.fq"
],
"outputs":
[
"SM10024.sai",
"SM10024.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10034.fq > SM10034.sai 2> SM10034.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10034.fq"
],
"outputs":
[
"SM10034.sai",
"SM10034.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10045.fq > SM10045.sai 2> SM10045.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10045.fq"
],
"outputs":
[
"SM10045.sai",
"SM10045.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10062.fq > SM10062.sai 2> SM10062.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10062.fq"
],
"outputs":
[
"SM10062.sai",
"SM10062.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10081.fq > SM10081.sai 2> SM10081.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10081.fq"
],
"outputs":
[
"SM10081.sai",
"SM10081.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10002.fq > SM10002.sai 2> SM10002.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10002.fq"
],
"outputs":
[
"SM10002.sai",
"SM10002.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10015.fq > SM10015.sai 2> SM10015.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10015.fq"
],
"outputs":
[
"SM10015.sai",
"SM10015.sai.err"
]
},
{
"command":"./bwa aln oak2.fa SM10025.fq > SM10025.sai 2> SM10025.sai.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10025.fq"
],
"outputs":
[
"SM10025.sai",
"SM10025.sai.err"
]
},
{
"command":"./bwa samse oak2.fa SM10001.sai SM10001.fq > SM10001.sam 2> SM10001.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10001.fq",
"SM10001.sai"
],
"outputs":
[
"SM10001.sam",
"SM10001.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10012.sai SM10012.fq > SM10012.sam 2> SM10012.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10012.fq",
"SM10012.sai"
],
"outputs":
[
"SM10012.sam",
"SM10012.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10024.sai SM10024.fq > SM10024.sam 2> SM10024.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10024.fq",
"SM10024.sai"
],
"outputs":
[
"SM10024.sam",
"SM10024.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10034.sai SM10034.fq > SM10034.sam 2> SM10034.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10034.fq",
"SM10034.sai"
],
"outputs":
[
"SM10034.sam",
"SM10034.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10045.sai SM10045.fq > SM10045.sam 2> SM10045.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10045.fq",
"SM10045.sai"
],
"outputs":
[
"SM10045.sam",
"SM10045.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10062.sai SM10062.fq > SM10062.sam 2> SM10062.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10062.fq",
"SM10062.sai"
],
"outputs":
[
"SM10062.sam",
"SM10062.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10081.sai SM10081.fq > SM10081.sam 2> SM10081.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10081.fq",
"SM10081.sai"
],
"outputs":
[
"SM10081.sam",
"SM10081.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10002.sai SM10002.fq > SM10002.sam 2> SM10002.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10002.fq",
"SM10002.sai"
],
"outputs":
[
"SM10002.sam",
"SM10002.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10015.sai SM10015.fq > SM10015.sam 2> SM10015.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10015.fq",
"SM10015.sai"
],
"outputs":
[
"SM10015.sam",
"SM10015.sam.err"
]
},
{
"command":"./bwa samse oak2.fa SM10025.sai SM10025.fq > SM10025.sam 2> SM10025.sam.err",
"inputs":
[
"./bwa",
"oak2.fa",
"oak2.fa.amb",
"oak2.fa.ann",
"oak2.fa.bwt",
"oak2.fa.sa",
"oak2.fa.pac",
"SM10025.fq",
"SM10025.sai"
],
"outputs":
[
"SM10025.sam",
"SM10025.sam.err"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10001.sam 2> SM10001_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10001.sam"
],
"outputs":
[
"SM10001_split.sam.err",
"SM10001.0.sam",
"SM10001.1.sam",
"SM10001.2.sam",
"SM10001.3.sam",
"SM10001.4.sam",
"SM10001.5.sam",
"SM10001.6.sam",
"SM10001.7.sam",
"SM10001.8.sam",
"SM10001.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10012.sam 2> SM10012_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10012.sam"
],
"outputs":
[
"SM10012_split.sam.err",
"SM10012.0.sam",
"SM10012.1.sam",
"SM10012.2.sam",
"SM10012.3.sam",
"SM10012.4.sam",
"SM10012.5.sam",
"SM10012.6.sam",
"SM10012.7.sam",
"SM10012.8.sam",
"SM10012.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10024.sam 2> SM10024_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10024.sam"
],
"outputs":
[
"SM10024_split.sam.err",
"SM10024.0.sam",
"SM10024.1.sam",
"SM10024.2.sam",
"SM10024.3.sam",
"SM10024.4.sam",
"SM10024.5.sam",
"SM10024.6.sam",
"SM10024.7.sam",
"SM10024.8.sam",
"SM10024.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10034.sam 2> SM10034_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10034.sam"
],
"outputs":
[
"SM10034_split.sam.err",
"SM10034.0.sam",
"SM10034.1.sam",
"SM10034.2.sam",
"SM10034.3.sam",
"SM10034.4.sam",
"SM10034.5.sam",
"SM10034.6.sam",
"SM10034.7.sam",
"SM10034.8.sam",
"SM10034.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10045.sam 2> SM10045_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10045.sam"
],
"outputs":
[
"SM10045_split.sam.err",
"SM10045.0.sam",
"SM10045.1.sam",
"SM10045.2.sam",
"SM10045.3.sam",
"SM10045.4.sam",
"SM10045.5.sam",
"SM10045.6.sam",
"SM10045.7.sam",
"SM10045.8.sam",
"SM10045.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10062.sam 2> SM10062_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10062.sam"
],
"outputs":
[
"SM10062_split.sam.err",
"SM10062.0.sam",
"SM10062.1.sam",
"SM10062.2.sam",
"SM10062.3.sam",
"SM10062.4.sam",
"SM10062.5.sam",
"SM10062.6.sam",
"SM10062.7.sam",
"SM10062.8.sam",
"SM10062.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10081.sam 2> SM10081_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10081.sam"
],
"outputs":
[
"SM10081_split.sam.err",
"SM10081.0.sam",
"SM10081.1.sam",
"SM10081.2.sam",
"SM10081.3.sam",
"SM10081.4.sam",
"SM10081.5.sam",
"SM10081.6.sam",
"SM10081.7.sam",
"SM10081.8.sam",
"SM10081.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10002.sam 2> SM10002_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10002.sam"
],
"outputs":
[
"SM10002_split.sam.err",
"SM10002.0.sam",
"SM10002.1.sam",
"SM10002.2.sam",
"SM10002.3.sam",
"SM10002.4.sam",
"SM10002.5.sam",
"SM10002.6.sam",
"SM10002.7.sam",
"SM10002.8.sam",
"SM10002.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10015.sam 2> SM10015_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10015.sam"
],
"outputs":
[
"SM10015_split.sam.err",
"SM10015.0.sam",
"SM10015.1.sam",
"SM10015.2.sam",
"SM10015.3.sam",
"SM10015.4.sam",
"SM10015.5.sam",
"SM10015.6.sam",
"SM10015.7.sam",
"SM10015.8.sam",
"SM10015.9.sam"
]
},
{
"command":"perl gatk_split_align 40000 oak2.fa SM10025.sam 2> SM10025_split.sam.err",
"inputs":
[
"gatk_split_align",
"oak2.fa",
"SM10025.sam"
],
"outputs":
[
"SM10025_split.sam.err",
"SM10025.0.sam",
"SM10025.1.sam",
"SM10025.2.sam",
"SM10025.3.sam",
"SM10025.4.sam",
"SM10025.5.sam",
"SM10025.6.sam",
"SM10025.7.sam",
"SM10025.8.sam",
"SM10025.9.sam"
]
},
{
"command":"./samtools view -bS SM10001.0.sam > SM10001.0.bam 2> SM10001.0.bam.err",
"inputs":
[
"./samtools",
"SM10001.0.sam"
],
"outputs":
[
"SM10001.0.bam",
"SM10001.0.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.1.sam > SM10001.1.bam 2> SM10001.1.bam.err",
"inputs":
[
"./samtools",
"SM10001.1.sam"
],
"outputs":
[
"SM10001.1.bam",
"SM10001.1.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.2.sam > SM10001.2.bam 2> SM10001.2.bam.err",
"inputs":
[
"./samtools",
"SM10001.2.sam"
],
"outputs":
[
"SM10001.2.bam",
"SM10001.2.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.3.sam > SM10001.3.bam 2> SM10001.3.bam.err",
"inputs":
[
"./samtools",
"SM10001.3.sam"
],
"outputs":
[
"SM10001.3.bam",
"SM10001.3.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.4.sam > SM10001.4.bam 2> SM10001.4.bam.err",
"inputs":
[
"./samtools",
"SM10001.4.sam"
],
"outputs":
[
"SM10001.4.bam",
"SM10001.4.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.5.sam > SM10001.5.bam 2> SM10001.5.bam.err",
"inputs":
[
"./samtools",
"SM10001.5.sam"
],
"outputs":
[
"SM10001.5.bam",
"SM10001.5.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.6.sam > SM10001.6.bam 2> SM10001.6.bam.err",
"inputs":
[
"./samtools",
"SM10001.6.sam"
],
"outputs":
[
"SM10001.6.bam",
"SM10001.6.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.7.sam > SM10001.7.bam 2> SM10001.7.bam.err",
"inputs":
[
"./samtools",
"SM10001.7.sam"
],
"outputs":
[
"SM10001.7.bam",
"SM10001.7.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.8.sam > SM10001.8.bam 2> SM10001.8.bam.err",
"inputs":
[
"./samtools",
"SM10001.8.sam"
],
"outputs":
[
"SM10001.8.bam",
"SM10001.8.bam.err"
]
},
{
"command":"./samtools view -bS SM10001.9.sam > SM10001.9.bam 2> SM10001.9.bam.err",
"inputs":
[
"./samtools",
"SM10001.9.sam"
],
"outputs":
[
"SM10001.9.bam",
"SM10001.9.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.0.sam > SM10012.0.bam 2> SM10012.0.bam.err",
"inputs":
[
"./samtools",
"SM10012.0.sam"
],
"outputs":
[
"SM10012.0.bam",
"SM10012.0.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.1.sam > SM10012.1.bam 2> SM10012.1.bam.err",
"inputs":
[
"./samtools",
"SM10012.1.sam"
],
"outputs":
[
"SM10012.1.bam",
"SM10012.1.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.2.sam > SM10012.2.bam 2> SM10012.2.bam.err",
"inputs":
[
"./samtools",
"SM10012.2.sam"
],
"outputs":
[
"SM10012.2.bam",
"SM10012.2.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.3.sam > SM10012.3.bam 2> SM10012.3.bam.err",
"inputs":
[
"./samtools",
"SM10012.3.sam"
],
"outputs":
[
"SM10012.3.bam",
"SM10012.3.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.4.sam > SM10012.4.bam 2> SM10012.4.bam.err",
"inputs":
[
"./samtools",
"SM10012.4.sam"
],
"outputs":
[
"SM10012.4.bam",
"SM10012.4.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.5.sam > SM10012.5.bam 2> SM10012.5.bam.err",
"inputs":
[
"./samtools",
"SM10012.5.sam"
],
"outputs":
[
"SM10012.5.bam",
"SM10012.5.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.6.sam > SM10012.6.bam 2> SM10012.6.bam.err",
"inputs":
[
"./samtools",
"SM10012.6.sam"
],
"outputs":
[
"SM10012.6.bam",
"SM10012.6.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.7.sam > SM10012.7.bam 2> SM10012.7.bam.err",
"inputs":
[
"./samtools",
"SM10012.7.sam"
],
"outputs":
[
"SM10012.7.bam",
"SM10012.7.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.8.sam > SM10012.8.bam 2> SM10012.8.bam.err",
"inputs":
[
"./samtools",
"SM10012.8.sam"
],
"outputs":
[
"SM10012.8.bam",
"SM10012.8.bam.err"
]
},
{
"command":"./samtools view -bS SM10012.9.sam > SM10012.9.bam 2> SM10012.9.bam.err",
"inputs":
[
"./samtools",
"SM10012.9.sam"