##fileformat=VCFv4.2
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (counting only informative reads out of the total reads) for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions for alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled posterior probabilities for genotypes as defined in the VCF specification">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=MB,Number=4,Type=Integer,Description="Per-sample component statistics to detect mate bias">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PRI,Number=G,Type=Float,Description="Phred-scaled prior probabilities for genotypes">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias">
##FORMAT=<ID=SQ,Number=A,Type=Float,Description="Somatic quality">
##DRAGENCommandLine=<ID=HashTableBuild,Version="SW: 01.003.044.3.10.4, HashTableVersion: 8",CommandLineOptions="dragen --build-hash-table true --ht-reference /staging/human/reference/hs37d5/hs37d5.fa --output-dir /staging/human/reference/hs37d5/hs37d5.fa.k_21.f_16.m_149 --ht-num-threads 32 --ht-seed-len 21 --enable-cnv true">
##DRAGENCommandLine=<ID=dragen,Version="SW: 07.021.624.3.10.9, HW: 07.021.624",Date="Fri Sep 15 14:27:23 CEST 2023",CommandLineOptions="--ref-dir /staging/human/reference/hs37d5/hs37d5.fa.k_21.f_16.m_149 --fastq-file1 /data/CASE_R1_001.fastq.gz --fastq-file2 /data/CASE_R2_001.fastq.gz --output-directory /data/CASE/ --output-file-prefix CASE_dragen --RGID WGS --RGSM CASE --RGLB CASE --num-threads 46 --enable-map-align true --enable-map-align-output true --enable-duplicate-marking true --generate-sa-tags true --generate-zs-tags true --vc-output-evidence-bam true --vc-evidence-bam-output-haplotypes true --vc-evidence-bam-force-output true --enable-variant-caller true --vc-emit-ref-confidence gvcf --vc-enable-vcf-output 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 --enable-cyp2d6 false --repeat-genotype-enable true --repeat-genotype-specs /home/helmuth/workspace/hum-dragen-routine.git/scripts/../resources/expansionhunter/GRCh37_edico+stripy+smn.json --enable-hla false --enable-smn false --qc-coverage-ignore-overlaps true --qc-coverage-region-1 /home/helmuth/workspace/hum-dragen-routine.git/scripts/../resources/padded_agilentv8_MT.bed --qc-coverage-reports-1 cov_report full_res --qc-coverage-filters-1 mapq<1,bq<0 --qc-coverage-region-2 /home/helmuth/workspace/hum-dragen-routine.git/scripts/../resources/difficult_regions.bed --qc-coverage-reports-2 cov_report full_res --qc-coverage-filters-2 mapq<1,bq<0 --qc-coverage-region-3 /home/helmuth/workspace/hum-dragen-routine.git/scripts/../resources/padded_agilentv8_MT.bed --qc-coverage-reports-3 cov_report full_res --qc-coverage-filters-3 mapq<0,bq<0">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (informative and non-informative); some reads may have been filtered based on mapq etc.">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=FractionInformativeReads,Number=1,Type=Float,Description="The fraction of informative reads out of the total reads">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##FILTER=<ID=DRAGENSnpHardQUAL,Description="Set if true:QUAL < 10.41">
##FILTER=<ID=DRAGENIndelHardQUAL,Description="Set if true:QUAL < 7.83">
##FILTER=<ID=LowDepth,Description="Set if true:DP <= 1">
##FILTER=<ID=LowGQ,Description="Set if true:GQ = 0">
##FILTER=<ID=PloidyConflict,Description="Genotype call from variant caller not consistent with chromosome ploidy">
##FILTER=<ID=base_quality,Description="Site filtered because median base quality of alt reads at this locus does not meet threshold">
##FILTER=<ID=filtered_reads,Description="Site filtered because too large a fraction of reads have been filtered out">
##FILTER=<ID=fragment_length,Description="Site filtered because absolute difference between the median fragment length of alt reads and median fragment length of ref reads at this locus exceeds threshold">
##FILTER=<ID=low_depth,Description="Site filtered because the read depth is too low">
##FILTER=<ID=low_frac_info_reads,Description="Site filtered because the fraction of informative reads is below threshold">
##FILTER=<ID=low_normal_depth,Description="Site filtered because the normal sample read depth is too low">
##FILTER=<ID=long_indel,Description="Site filtered because the indel length is too long">
##FILTER=<ID=mapping_quality,Description="Site filtered because median mapping quality of alt reads at this locus does not meet threshold">
##FILTER=<ID=multiallelic,Description="Site filtered because more than two alt alleles pass tumor LOD">
##FILTER=<ID=non_homref_normal,Description="Site filtered because the normal sample genotype is not homozygous reference">
##FILTER=<ID=no_reliable_supporting_read,Description="Site filtered because no reliable supporting somatic read exists">
##FILTER=<ID=panel_of_normals,Description="Seen in at least one sample in the panel of normals vcf">
##FILTER=<ID=read_position,Description="Site filtered because median of distances between start/end of read and this locus is below threshold">
##FILTER=<ID=RMxNRepeatRegion,Description="Site filtered because all or part of the variant allele is a repeat of the reference">
##FILTER=<ID=str_contraction,Description="Site filtered due to suspected PCR error where the alt allele is one repeat unit less than the reference">
##FILTER=<ID=too_few_supporting_reads,Description="Site filtered because there are too few supporting reads in the tumor sample">
##FILTER=<ID=weak_evidence,Description="Somatic variant score does not meet threshold">
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##reference=file:///staging/human/reference/hs37d5/hs37d5.fa.k_21.f_16.m_149/reference.bin
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CASE
17	41256074	.	CA	C	49.57	PASS	AC=1;AF=0.500;AN=2;DP=40;FS=1.397;MQ=249.24;MQRankSum=4.084;QD=1.24;ReadPosRankSum=1.804;SOR=1.051;FractionInformativeReads=0.800	GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS	0|1:18,14:0.438:32:9,10:9,4:47:60,0,47:4.9567e+01,9.1418e-05,5.0000e+01:0.00,10.00,13.01:10,8,9,5:9,9,9,5:41256074
MT	750	.	A	G	.	PASS	DP=5639;MQ=150.72;FractionInformativeReads=0.995	GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB	1/1:98.13:1,5607:1.000:0,2721:1,2886:5608:0,1,3291,2316:1,0,2879,2728