## htsjdk.samtools.metrics.StringHeader
# au.edu.wehi.idsv.Idsv INPUT=[/mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0081_BC0GHHACXX_7_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0081_BC0GHHACXX_8_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0080_AD0JHUACXX_8_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100R/CPCG_0100_Ly_R_PE_469_WG_120201_h803_0080_AD0JHUACXX_7_NoIndex.markdup.bam] INPUT_TUMOUR=[/mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_3_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_6_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_5_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_2_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_4_NoIndex.markdup.bam, /mnt/bam/CPCG0100/CPCG0100P/CPCG_0100_Pr_P_PE_448_WG_120201_h803_0081_BC0GHHACXX_1_NoIndex.markdup.bam] OUTPUT=/mnt/bam/CPCG0100/CPCG0100.vcf REFERENCE=/mnt/reference/hg19/hg19_random.fa SCRIPT=/mnt/bam/CPCG0100/gridss/realign.sh PER_CHR=true WORKING_DIR=/mnt/bam/CPCG0100/gridss CALL_ONLY_ASSEMBLIES=true TMP_DIR=[/mnt/bam/CPCG0100/gridss] VERBOSITY=DEBUG    STEPS=[CALCULATE_METRICS, EXTRACT_SOFT_CLIPS, EXTRACT_READ_PAIRS, ASSEMBLE_BREAKENDS, REALIGN_SOFT_CLIPS, REALIGN_ASSEMLIES, SORT_REALIGNED_SOFT_CLIPS, SORT_REALIGNED_ASSEMBLIES, CALL_STRUCTURAL_VARIANTS, ANNOTATE_VARIANTS] SOFT_CLIP_MIN_LENGTH=4 READ_PAIR_ANCHOR_MIN_MAPQ=5 SOFT_CLIP_MIN_MAPQ=5 SOFT_CLIP_MIN_ANCHOR_PERCENT_IDENTITY=95.0 ASSEMBLY_METHOD=DEBRUIJN_SUBGRAPH ASSEMBLY_DEBRUIJN_KMER=25 ASSEMBLY_DEBRUIJN_MAX_PATH_COLLAPSE_BASE_MISMATCHES=2 ASSEMBLY_DEBRUIJN_COLLAPSE_BUBBLES_ONLY=false ASSEMBLY_DEBRUIJN_ALLOW_REFERENCE_KMER_RESUSE=true ASSEMBLY_DEBRUIJN_MAX_CONTIGS_PER_ITERATION=1024 ASSEMBLY_DEBRUIJN_SUBGRAPH_BRANCHING_FACTOR=16 ASSEMBLY_DEBRUIJN_SUBGRAPH_ASSEMBLY_FRAGMENT_DELAY=3.0 REALIGNMENT_MIN_BREAKEND_LENGTH=20 REALIGNMENT_MIN_BASE_QUALITY=5.0 REALIGNMENT_MAPQ_UNIQUE_THRESHOLD=10 SOMATIC_THRESHOLD=0.001 MIN_INDEL_SIZE=16 VCF41_COMPATIBLE=true QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Oct 29 03:01:08 UTC 2014

## METRICS CLASS	gridss.analysis.IdsvMetrics
MAX_READ_LENGTH	MAX_PROPER_PAIR_FRAGMENT_LENGTH
101	651


