Hi GATK team.
FYI:
when using DepthOfCoverage 3.6.0 using the following arguments:
-T DepthOfCoverage -R $(REF) --validation_strictness LENIENT -L:capture,BED in.bed -I in.al --outputFormat csv -o out.tsv --omitIntervalStatistics --omitPerSampleStats --omitLocusTable
the first line of the header looks tab delimited
Locus Total_Depth Average_Depth_sample Depth_for_SAMPLE
while the remaining lines are comma delimited
1:1116653,116,116.00,116
Regards,
Pierre