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163 bytes added
, 14:51, 30 June 2015
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| * BATCH_TYPE | | * BATCH_TYPE |
| * IGNORE_SM_CHECK - turn off the default validation that the @RG SM tag matches the bam list sample name. | | * IGNORE_SM_CHECK - turn off the default validation that the @RG SM tag matches the bam list sample name. |
− | * IGNORE_REF_CHR_CHECK | + | * IGNORE_REF_CHR_CHECK - turn off the default validation that checks that all of the BAM's chromosomes are in the reference file - eventually we may update to just validate those in CHRS. |
| * OUT_DIR | | * OUT_DIR |
| * BAM_LIST | | * BAM_LIST |
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| * The BAM_LIST file can contain config values within it - the overall pipeline section will be checked for those config values. | | * The BAM_LIST file can contain config values within it - the overall pipeline section will be checked for those config values. |
| * By default if a value is not defined in the section, it will check global. | | * By default if a value is not defined in the section, it will check global. |
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| ==== Configure Each Step ==== | | ==== Configure Each Step ==== |