When NOT using the -s surveillance flag the code derived from Escape_Variants.mdGATK step 11 is run.
The output files created by this code do not get copied to the output directory.
Do we need to save these files when not running in surveillance mode?
Details
GATK step 11 Compile all tab tables into one for depth and genotype consists of three scripts:
run-bcftools-query-alt-ad.sh which creates files with filename patterns $root.filt.tab and $root.depth.tab.
run-depth-compiler.sh which creates a file named alldepths.final.tabrun-genotype-compiler.sh which creates a file named allgenotypes.final.tab
When NOT using the
-s
surveillance flag the code derived from Escape_Variants.mdGATK step 11
is run. The output files created by this code do not get copied to the output directory. Do we need to save these files when not running in surveillance mode?Details
GATK step 11
Compile all tab tables into one for depth and genotype
consists of three scripts: run-bcftools-query-alt-ad.sh which creates files with filename patterns$root.filt.tab
and$root.depth.tab
. run-depth-compiler.sh which creates a file namedalldepths.final.tab
run-genotype-compiler.sh which creates a file namedallgenotypes.final.tab