##fileformat=VCFv4.1
##fileDate=20220321
##source=DRAGEN 07.021.624.3.10.4
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##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=DUPSVLEN,Number=.,Type=Integer,Description="Length of duplicated reference sequence">
##INFO=<ID=DUPSVINSLEN,Number=.,Type=Integer,Description="Length of inserted sequence after duplicated reference sequence">
##INFO=<ID=DUPSVINSSEQ,Number=.,Type=String,Description="Inserted sequence after duplicated reference sequence">
##INFO=<ID=DUPHOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints excluding duplicated reference sequence">
##INFO=<ID=DUPHOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints excluding duplicated reference sequence">
##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
##INFO=<ID=JUNCTION_QUAL,Number=1,Type=Integer,Description="If the SV junction is part of an EVENT (ie. a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999">
##FILTER=<ID=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation (not applied to records with KnownSVScoring flag)">
##FILTER=<ID=MaxDepth,Description="Depth is greater than 3x the median chromosome depth near one or both variant breakends (not applied to records with KnownSVScoring flag)">
##FILTER=<ID=MaxMQ0Frac,Description="For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4 (not applied to records with KnownSVScoring flag)">
##FILTER=<ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample (not applied to records with KnownSVScoring flag)">
##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20 (not applied to records with KnownSVScoring flag)">
##FILTER=<ID=SampleFT,Description="No sample passes all the sample-level filters">
##FILTER=<ID=MinGQ,Description="GQ score is less than 5 (filter applied at sample level; not applied to records with KnownSVScoring flag)">
##FILTER=<ID=HomRef,Description="homozygous reference call (filter applied at sample level)">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##cmdline=dragen --ref-dir /staging/human/reference/hs37d5/hs37d5.fa.k_21.f_16.m_149 --fastq-file1 /mnt/smb01-hum/NGSRawData/220318_A01077_0174_AH7JGVDMXY/Data/Intensities/BaseCalls/NA-12878WGS-Genom-size_S1_R1_001.fastq.gz --fastq-file2 /mnt/smb01-hum/NGSRawData/220318_A01077_0174_AH7JGVDMXY/Data/Intensities/BaseCalls/NA-12878WGS-Genom-size_S1_R2_001.fastq.gz --output-directory /staging/output/220318_A01077_0174_AH7JGVDMXY/NA-12878WGSWGS/ --output-file-prefix NA-12878WGSWGS_dragen --RGID WGS --RGSM NA-12878WGSWGS --num-threads 46 --enable-map-align true --enable-map-align-output true --enable-duplicate-marking true --enable-variant-caller true --qc-cross-cont-vcf /opt/edico/config/sample_cross_contamination_resource_GRCh37.vcf.gz --enable-cnv true --cnv-enable-self-normalization true --enable-sv true --qc-coverage-region-1 /staging/human/bed/CDS-v19-ROIs_v2.bed --qc-coverage-reports-1 cov_report full_res --qc-coverage-region-2 /staging/human/bed/Regions_Exomev8.bed --qc-coverage-reports-2 cov_report full_res --qc-coverage-region-3 /staging/human/bed/Padded_Exomev8.bed --qc-coverage-reports-3 cov_report full_res
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
1	1598413	MantaDEL:19042:0:0:0:0:0	ACACGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTCAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCAAACCAGAGAAATCCAGCTCTGGGTGACAGAGCAAGACTCTGTTTCGGGAAAAATAAAATACATAGGCAGGGCGCGGTGGCT	A	762	PASS	END=1598580;SVTYPE=DEL;SVLEN=-167;CIGAR=1M167D;CIPOS=0,18;HOMLEN=18;HOMSEQ=CACGCCTGTAATCCCAGC	GT:FT:GQ:PL:PR:SR	1/1:PASS:53:815,56,0:0,2:0,20