gatk_cnv step 3 has the potential of attempting to interpret log2 of 0

[bryce-turner]

gatk_cnv step 3 has the potential of attempting to interpret log2 of 0. This is a rare edge case where the count for the interval is 0 and is not filtered out in any of the previous steps.

phoenix/modules/somatic/gatk_cnv.jst

Lines 424 to 440 in 9f04da2

	gatk --java-options "-Xmx12g" CreateReadCountPanelOfNormals \
	--tmp-dir {{ temp_dir }}/temp3/ \
	--input {{ temp_dir }}/{{ pair.normal.name }}.{{ aligner }}.counts.hdf5 \
	--minimum-interval-median-percentile 0.0 \
	--annotated-intervals {{ temp_dir }}/anno_preprocessed.interval_list \
	--output {{ temp_dir }}/cnv.pon.hdf5
	{# Make working and temp directories #}
	mkdir -p "{{ temp_dir }}/temp4"
	{# Denoise the tumor using the panel of normals made from the matched normal #}
	gatk --java-options "-Xmx12g" DenoiseReadCounts \
	--tmp-dir {{ temp_dir }}/temp4/ \
	--input {{ temp_dir }}/{{ pair.tumor.name }}.{{ aligner }}.counts.hdf5 \
	--count-panel-of-normals {{ temp_dir }}/cnv.pon.hdf5 \
	--standardized-copy-ratios {{ results_dir }}/{{ pair.name }}.{{ aligner }}.standardizedCR.tsv \
	--denoised-copy-ratios {{ results_dir }}/{{ pair.name }}.{{ aligner }}.denoisedCR.tsv

One solution to this is setting the --minimum-interval-median-percentile to be really small, since this can use scientific notation a value such as 1E-30 would work and avoid 0's being passed into a log2 calculation.