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graph.dot
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digraph G {
n39[label="BAMS", color="red"];
n9[label="SS.11.01_P_nsort.bam", color="red"];
n42[label="SS.11.01_U_nsort.bam", color="red"];
n6[label="SS.11.01_dupmrk.bam", color="red"];
n7[label="SS.11.01_fixed.bam", color="red"];
n8[label="SS.11.01_merged.bam", color="red"];
n63[label="SS.11.02_P_nsort.bam", color="red"];
n47[label="SS.11.02_U_nsort.bam", color="red"];
n60[label="SS.11.02_dupmrk.bam", color="red"];
n61[label="SS.11.02_fixed.bam", color="red"];
n62[label="SS.11.02_merged.bam", color="red"];
n56[label="GVCF", color="red"];
n4[label="CHROM_JOBS", color="red"];
n5[label="SS.11.01.g.vcf.gz", color="red"];
n59[label="SS.11.02.g.vcf.gz", color="red"];
n3[label="res.vcf.gz", color="red"];
n22[label="REF", color="red"];
n58[label="genome.dict", color="red"];
n19[label="genome.fasta", color="red"];
n65[label="genome.intervals.txt", color="red"];
n36[label="SAMS", color="red"];
n10[label="SS.11.01_P.sam", color="red"];
n43[label="SS.11.01_U.sam", color="red"];
n64[label="SS.11.02_P.sam", color="red"];
n48[label="SS.11.02_U.sam", color="red"];
n14[label="TRIM", color="red"];
n11[label="SS.11.01_1P.fq.gz", color="red"];
n44[label="SS.11.01_1U.fq.gz", color="red"];
n32[label="SS.11.01_2P.fq.gz", color="red"];
n45[label="SS.11.01_2U.fq.gz", color="red"];
n33[label="SS.11.02_1P.fq.gz", color="red"];
n49[label="SS.11.02_1U.fq.gz", color="red"];
n35[label="SS.11.02_2P.fq.gz", color="red"];
n46[label="SS.11.02_2U.fq.gz", color="red"];
n2[label="all", color="red"];
n25[label="bt2-index", color="red"];
n17[label="Ssc.1.bt2", color="red"];
n27[label="Ssc.2.bt2", color="red"];
n28[label="Ssc.3.bt2", color="red"];
n29[label="Ssc.4.bt2", color="red"];
n30[label="Ssc.rev.1.bt2", color="red"];
n31[label="Ssc.rev.2.bt2", color="red"];
n20[label="GCA_001857865.1_ASM185786v1_genomic.fna.gz", color="green"];
n21[label="sclerotinia_sclerotiorum_mitochondria_2_contigs.fasta.gz", color="green"];
n12[label="SS.11.01_1.fq.gz", color="green"];
n34[label="SS.11.02_1.fq.gz", color="green"];
n23[label="runs", color="red"];
n26[label="BOWTIE2-BUILD", color="red"];
n18[label="jobid.txt", color="red"];
n73[label="CHROM_RUN", color="red"];
n68[label="GATK-INTERVALS", color="red"];
n55[label="GATK-REF", color="red"];
n57[label="MAKE-GVCF", color="red"];
n72[label="MAKE-VCF", color="red"];
n37[label="MAP-READS", color="red"];
n53[label="MARK-DUPS", color="red"];
n50[label="MERGE-BAMS", color="red"];
n40[label="SAM-TO-BAM", color="red"];
n15[label="TRIM-READS", color="red"];
n70[label="CAT-VCF.sh", color="green"];
n51[label="add-MD-tag.sh", color="green"];
n71[label="chromosome-jobs.sh", color="green"];
n66[label="make-GATK-intervals.py", color="green"];
n67[label="make-GATK-intervals.sh", color="green"];
n54[label="make-GVCF.sh", color="green"];
n69[label="make-VCF.sh", color="green"];
n16[label="make-alignment.sh", color="green"];
n24[label="make-index.sh", color="green"];
n52[label="mark-duplicates.sh", color="green"];
n41[label="merge-bam.sh", color="green"];
n38[label="sam-to-bam.sh", color="green"];
n13[label="trim-reads.sh", color="green"];
n39 -> n9 ;
n10 -> n9 ;
n40 -> n9 ;
n38 -> n9 ;
n39 -> n42 ;
n43 -> n42 ;
n40 -> n42 ;
n38 -> n42 ;
n7 -> n6 ;
n53 -> n6 ;
n52 -> n6 ;
n8 -> n7 ;
n51 -> n7 ;
n9 -> n8 ;
n42 -> n8 ;
n47 -> n8 ;
n50 -> n8 ;
n41 -> n8 ;
n39 -> n63 ;
n64 -> n63 ;
n40 -> n63 ;
n38 -> n63 ;
n39 -> n47 ;
n48 -> n47 ;
n40 -> n47 ;
n38 -> n47 ;
n61 -> n60 ;
n53 -> n60 ;
n52 -> n60 ;
n62 -> n61 ;
n51 -> n61 ;
n42 -> n62 ;
n63 -> n62 ;
n47 -> n62 ;
n50 -> n62 ;
n41 -> n62 ;
n5 -> n4 ;
n59 -> n4 ;
n65 -> n4 ;
n73 -> n4 ;
n72 -> n4 ;
n70 -> n4 ;
n71 -> n4 ;
n69 -> n4 ;
n6 -> n5 ;
n56 -> n5 ;
n58 -> n5 ;
n19 -> n5 ;
n57 -> n5 ;
n54 -> n5 ;
n60 -> n59 ;
n56 -> n59 ;
n58 -> n59 ;
n57 -> n59 ;
n54 -> n59 ;
n4 -> n3 ;
n19 -> n58 ;
n55 -> n58 ;
n22 -> n19 ;
n20 -> n19 ;
n21 -> n19 ;
n23 -> n19 ;
n19 -> n65 ;
n68 -> n65 ;
n66 -> n65 ;
n67 -> n65 ;
n36 -> n10 ;
n11 -> n10 ;
n32 -> n10 ;
n35 -> n10 ;
n17 -> n10 ;
n27 -> n10 ;
n28 -> n10 ;
n29 -> n10 ;
n30 -> n10 ;
n31 -> n10 ;
n37 -> n10 ;
n16 -> n10 ;
n36 -> n43 ;
n44 -> n43 ;
n45 -> n43 ;
n46 -> n43 ;
n17 -> n43 ;
n27 -> n43 ;
n28 -> n43 ;
n29 -> n43 ;
n30 -> n43 ;
n31 -> n43 ;
n37 -> n43 ;
n16 -> n43 ;
n36 -> n64 ;
n32 -> n64 ;
n33 -> n64 ;
n35 -> n64 ;
n17 -> n64 ;
n27 -> n64 ;
n28 -> n64 ;
n29 -> n64 ;
n30 -> n64 ;
n31 -> n64 ;
n37 -> n64 ;
n16 -> n64 ;
n36 -> n48 ;
n45 -> n48 ;
n49 -> n48 ;
n46 -> n48 ;
n17 -> n48 ;
n27 -> n48 ;
n28 -> n48 ;
n29 -> n48 ;
n30 -> n48 ;
n31 -> n48 ;
n37 -> n48 ;
n16 -> n48 ;
n14 -> n11 ;
n12 -> n11 ;
n15 -> n11 ;
n13 -> n11 ;
n11 -> n44 ;
n33 -> n44 ;
n11 -> n32 ;
n33 -> n32 ;
n11 -> n45 ;
n33 -> n45 ;
n14 -> n33 ;
n34 -> n33 ;
n15 -> n33 ;
n13 -> n33 ;
n11 -> n49 ;
n33 -> n49 ;
n11 -> n35 ;
n33 -> n35 ;
n11 -> n46 ;
n33 -> n46 ;
n3 -> n2 ;
n18 -> n17 ;
n18 -> n27 ;
n18 -> n28 ;
n18 -> n29 ;
n18 -> n30 ;
n18 -> n31 ;
n19 -> n18 ;
n25 -> n18 ;
n26 -> n18 ;
n24 -> n18 ;
}