##fileformat=VCFv4.1
##fileDate=20220907
##source=GenerateSVCandidates 1.6.0
##reference=file:///fast/projects/cubit/20.05/static_data/reference/GRCh37/hs37d5/hs37d5.fa
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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=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">
##FILTER=<ID=MaxDepth,Description="Depth is greater than 3x the median chromosome depth near one or both variant breakends">
##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">
##FILTER=<ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample.">
##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20">
##FILTER=<ID=SampleFT,Description="No sample passes all the sample-level filters (at the field FORMAT/FT)">
##FILTER=<ID=MinGQ,Description="GQ score is less than 15 (filter applied at sample level)">
##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=configManta.py --referenceFasta /fast/projects/cubit/20.05/static_data/reference/GRCh37/hs37d5/hs37d5.fa --runDir work/bwa.manta.SAMPLE-N1-DNA1-WGS1/work --bam ngs_mapping/output/bwa.SAMPLE-N1-DNA1-WGS1/out/bwa.SAMPLE-N1-DNA1-WGS1.bam
#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