## htsjdk.samtools.metrics.StringHeader
# CollectRrbsMetrics  --INPUT data/3A_WT_WGBS_chr2_17k R1_sorted.bam --METRICS_FILE_PREFIX 3A_WT_WGBS --MINIMUM_READ_LENGTH 5 --C_QUALITY_THRESHOLD 20 --NEXT_BASE_QUALITY_THRESHOLD 10 --MAX_MISMATCH_RATE 0.1 --ASSUME_SORTED true --VALIDATION_STRINGENCY STRICT --REFERENCE data/hg19_chr2_17k.fasta  --METRIC_ACCUMULATION_LEVEL ALL_READS --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Feb 04 21:39:23 UTC 2020

## METRICS CLASS	picard.analysis.RrbsSummaryMetrics
READS_ALIGNED	NON_CPG_BASES	NON_CPG_CONVERTED_BASES	PCT_NON_CPG_BASES_CONVERTED	CPG_BASES_SEEN	CPG_BASES_CONVERTED	PCT_CPG_BASES_CONVERTED	MEAN_CPG_COVERAGE	MEDIAN_CPG_COVERAGE	READS_WITH_NO_CPG	READS_IGNORED_SHORT	READS_IGNORED_MISMATCHES	SAMPLE	LIBRARY	READ_GROUP
1397	14387	14073	0.978175	803	364	0.4533	7.872549	3	786	0	87			


