##fileformat=VCFv4.2
##FILTER=<ID=FREQ,Description="Depth-only copy number record whose AF value is higher than user specified threshold">
##FILTER=<ID=LOW_QS,Description="Depth-only copy number record whose QS value is lower than user specified threshold">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Segment most-likely copy-number call">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Segment genotype">
##FORMAT=<ID=NP,Number=1,Type=Integer,Description="Number of points (i.e. targets or bins) in the segment">
##FORMAT=<ID=QA,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that all points (i.e. targets or bins) in the segment agree with the segment copy-number call">
##FORMAT=<ID=QS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that at least one point (i.e. target or bin) in the segment agrees with the segment copy-number call">
##FORMAT=<ID=QSE,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that the segment end position is a genuine copy-number changepoint">
##FORMAT=<ID=QSS,Number=1,Type=Integer,Description="Complementary Phred-scaled probability that the segment start position is a genuine copy-number changepoint">
##GATKCommandLine=<ID=JointGermlineCNVSegmentation,CommandLine="JointGermlineCNVSegmentation --model-call-intervals work/gcnv_preprocess_intervals.Agilent_SureSelect_Human_All_Exon_V8/out/gcnv_preprocess_intervals.Agilent_SureSelect_Human_All_Exon_V8.interval_list --output work/bwa_mem2.gcnv.LB23_1253-N1-DNA1-WES1/out/bwa_mem2.gcnv.LB23_1253-N1-DNA1-WES1.vcf.gz --pedigree work/write_pedigree.LB23_1253-N1-DNA1-WES1/out/LB23_1253-N1-DNA1-WES1.ped --variant work/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1/out/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1.vcf.gz --variant work/bwa_mem2.gcnv_post_germline_calls.LB23_1254-N1-DNA1-WES1/out/bwa_mem2.gcnv_post_germline_calls.LB23_1254-N1-DNA1-WES1.vcf.gz --variant work/bwa_mem2.gcnv_post_germline_calls.LB23_1255-N1-DNA1-WES1/out/bwa_mem2.gcnv_post_germline_calls.LB23_1255-N1-DNA1-WES1.vcf.gz --reference /data/cephfs-1/work/projects/cubit/20.05/reference/GRCh37/hs37d5/hs37d5.fa --minimum-qs-score 20 --min-sample-set-fraction-overlap 0.0 --defragmentation-padding-fraction 0.25 --clustering-interval-overlap 0.8 --clustering-breakend-window 0 --breakpoint-summary-strategy MEDIAN_START_MEDIAN_END --alt-allele-summary-strategy COMMON_SUBTYPE --autosomal-ref-copy-number 2 --ignore-variants-starting-outside-interval false --combine-variants-distance 0 --max-distance 2147483647 --ref-padding 1 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.3.0.0",Date="April 19, 2023 at 9:52:14 AM CEST">
##GATKCommandLine=<ID=PostprocessGermlineCNVCalls,CommandLine="PostprocessGermlineCNVCalls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0032_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0032_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0034_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0034_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0031_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0031_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0028_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0028_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0004_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0004_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0019_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0019_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0005_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0005_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0035_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0035_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0002_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0002_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0036_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0036_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0018_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0018_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0012_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0012_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0033_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0033_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0025_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0025_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0010_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0010_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0024_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0024_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0023_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0023_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0007_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0007_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0020_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0020_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0021_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0021_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0015_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0015_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0022_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0022_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0017_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0017_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0030_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0030_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0014_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0014_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0006_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0006_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0013_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0013_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0011_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0011_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0001_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0001_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0026_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0026_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0003_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0003_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0008_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0008_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0029_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0029_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0009_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0009_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0016_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0016_of_36/cnv_calls-calls --calls-shard-path work/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0027_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelect_Human_All_Exon_V8.0027_of_36/cnv_calls-calls --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0032_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0032_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0034_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0034_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0031_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0031_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0028_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0028_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0004_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0004_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0019_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0019_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0005_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0005_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0035_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0035_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0002_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0002_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0036_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0036_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0018_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0018_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0012_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0012_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0033_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0033_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0025_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0025_of_36/cnv_calls-model --model-shard-path 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/data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0007_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0007_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0020_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0020_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0021_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0021_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0015_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0015_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0022_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0022_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0017_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0017_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0030_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0030_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0014_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0014_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0006_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0006_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0013_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0013_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0011_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0011_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0001_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0001_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0026_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0026_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0003_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0003_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0008_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0008_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0029_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0029_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0009_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0009_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0016_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0016_of_36/cnv_calls-model --model-shard-path /data/cephfs-1/work/projects/medgen_cads/STATIC_DATA/2023-01-17_GCNV_Agilent_SureSelectXT_Human_All_Exon_V8/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0027_of_36/out/bwa_mem2.gcnv_call_cnvs.Agilent_SureSelectXT_Human_All_Exon_V8.0027_of_36/cnv_calls-model --contig-ploidy-calls work/bwa_mem2.gcnv_contig_ploidy.Agilent_SureSelect_Human_All_Exon_V8/out/bwa_mem2.gcnv_contig_ploidy.Agilent_SureSelect_Human_All_Exon_V8/ploidy-calls --sample-index 0 --autosomal-ref-copy-number 2 --allosomal-contig X --allosomal-contig Y --output-genotyped-intervals work/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1/out/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1.interval.vcf --output-genotyped-segments work/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1/out/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1.vcf --output-denoised-copy-ratios work/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1/out/bwa_mem2.gcnv_post_germline_calls.LB23_1253-N1-DNA1-WES1.ratio.tsv --het-deletion-qs-threshold 100 --hom-deletion-qs-threshold 400 --duplication-qs-threshold 50 --site-frequency-threshold 0.01 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.3.0.0",Date="April 19, 2023 at 9:49:52 AM CEST">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AC_Orig,Number=A,Type=Integer,Description="Original AC">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AF_Orig,Number=A,Type=Float,Description="Original AF">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AN_Orig,Number=1,Type=Integer,Description="Original AN">
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate of the variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
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##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
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##contig=<ID=GL000248.1,length=39786>
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##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
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##contig=<ID=GL000225.1,length=211173>
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##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##gcnvVcfSchemaVersion=2.0
##source=JointGermlineCNVSegmentation
##source=PostprocessGermlineCNVCalls
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
1	4124001	.	N	<DEL>	.	.	END=4125000;SVTYPE=DEL;SVLEN=-999;AC=1;AN=1	GT:CN:NP:QA:QS:QSE:QSS	1:1:1:107:107:107:107