Switch to tabs for filter output #2
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Also adds filtered `del` files.
This makes all files uniform bed format files.
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I also just changed to add "chr" to manta and freec output from the awk step so that we can use these output files for bedtools. |
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I changed the output of step 2 to tab separated to ease later potential transition to bedtools (and so the output bed files are proper bed files).
I also made sure we were creating all dup and del filtered files for testing.