mutect.template

#####
# If generating JSON for multiple samples, replace '</full/file/path>' or 'null' with '<>', then complete mutect.sample_list.tab. See
# ./backup_templates/mutect.sample_list.template for examples. Be certain to provide a unique identifier under the 'run_uid' header to
# clearly distinguish samples/runs. If *optional* sample-specific values are desired, the appropriate key from this template may be used as
# a column header in mutect.sample_list.tab (be careful to maintain tab-delimited format).
####
tumor: {
    class: File
    path: <full/file/path>          # Required file; replace '</full/file/path>' with full path to tumor DNA BAM file [e.g., /my/path/to/tumor.bam]
normal: {
    class: File
    path: <full/file/path>          # Required file; replace '</full/file/path>' with full path to normal DNA BAM file [e.g., /my/path/to/normal.bam]
reference: {
    class: File
    path: </full/file/path>         # Required file; replace '</full/file/path>' with full path to uncompressed reference FASTA [e.g., /my/path/to/genome.fa]
cosmic: {
    class: File
    path: </full/file/path>         # Required file; replace '</full/file/path>' with full path to COSMIC VCF file [e.g., /my/path/to/cosmic.vcf]
dbsnp: {
    class: File
    path: </full/file/path>         # Required file; replace '</full/file/path>' with full path to dbSNP VCF file [e.g., /my/path/to/dbsnp.vcf]
vcf: null                           # Optional string; name of file to write stats; 'null' defaults to 'mutect.vcf'
coverage_file: null                 # Optional string; name of output coverage WIG file; 'null' defaults to 'mutect_coverage.wig.txt'
out: null                           # Optional string; name of file to write stats; 'null' defaults to 'mutect_call_stats.txt'
tumor_lod: null                     # Optional float; 'null' defaults to '6.3'
initial_tumor_lod: null             # Optional float; 'null' defaults to '4.0'
ncpus: null                         # Optional integer; number of threads to run MuTect; 'null' defaults to '8'