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wodanaz / Assembling_viruses

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Save GATK step 11 output #21

Closed johnbradley closed 3 years ago

johnbradley commented 3 years ago

When NOT using the -s surveillance flag the code derived from Escape_Variants.md GATK 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.tab run-genotype-compiler.sh which creates a file named allgenotypes.final.tab

wodanaz commented 3 years ago

Yes, we need to save these files in addition to the compiled tables.

Thanks!