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discovery_variables.yml
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name: discovery_variables
python: /ihome/gway/.conda/envs/pdx-exomeseq/bin/python
java: /opt/java/jdk1.7.0_79/bin/java
r: /ihome/gway/.conda/envs/pdx-exomeseq/bin/Rscript
condaenv: pdx-exomeseq
hgreference: /lorax/sanchezlab/shared/pdx_exomeseq/reference/human_g1k_v37.fasta
mmreference: /lorax/sanchezlab/shared/pdx_exomeseq/reference/mm9.fa
combinedref: /lorax/sanchezlab/shared/pdx_exomeseq/reference/combined_g1k_v37_mm9.fasta
dbsnp: /lorax/sanchezlab/shared/pdx_exomeseq/reference/dbsnp_138.b37.vcf
exonbed: /lorax/sanchezlab/shared/pdx_exomeseq/reference/exon_data.bed
directory: /lorax/sanchezlab/shared/pdx_exomeseq
fastqc: /ihome/gway/.conda/envs/pdx-exomeseq/bin/fastqc
multiqc: /ihome/gway/.conda/envs/pdx-exomeseq/bin/multiqc
cutadapt: /ihome/gway/.conda/envs/pdx-exomeseq/bin/cutadapt
trimgalore: /ihome/gway/.conda/envs/pdx-exomeseq/bin/trim_galore
bwa: /ihome/gway/.conda/envs/pdx-exomeseq/bin/bwa
samtools: /ihome/gway/.conda/envs/pdx-exomeseq/bin/samtools
picard: /ihome/gway/.conda/envs/pdx-exomeseq/bin/picard
gatk: /ihome/gway/.conda/envs/pdx-exomeseq/bin/gatk3
disambiguate: /ihome/gway/.conda/envs/pdx-exomeseq/bin/ngs_disambiguate
mosdepth: /ihome/gway/.conda/envs/pdx-exomeseq/bin/mosdepth