##fileformat=VCFv4.0
##fileDate=2016-06-21
##source=Platypus_Version_0.8.1
##platypusOptions={'assemblyRegionSize': 1500, 'trimReadFlank': 0, 'assembleBadReads': 1, 'bamFiles': ['/data/TCGA-A2-A0YC/tumor.bam'], 'minVarDist': 9, 'trimSoftClipped': 1, 'minReads': 2, 'qualBinSize': 1, 'refFile': '/data/ref_genome/human_g1k_v37.fasta', 'maxHaplotypes': 50, 'filterVarsByCoverage': 1, 'maxSize': 1500, 'originalMaxHaplotypes': 50, 'skipDifficultWindows': 0, 'parseNCBI': 0, 'skipRegionsFile': None, 'noCycles': 0, 'trimAdapter': 1, 'minPosterior': 5, 'assembleAll': 1, 'trimOverlapping': 1, 'filterDuplicates': 1, 'abThreshold': 0.001, 'minFlank': 10, 'bufferSize': 100000, 'fileCaching': 0, 'useEMLikelihoods': 0, 'coverageSamplingLevel': 30, 'calculateFlankScore': 0, 'logFileName': 'log.txt', 'nCPU': 1, 'filterReadsWithUnmappedMates': 1, 'qdThreshold': 10, 'maxVariants': 8, 'scThreshold': 0.95, 'filterReadsWithDistantMates': 1, 'maxReads': 5000000, 'badReadsWindow': 11, 'genIndels': 1, 'largeWindows': 0, 'minMapQual': 20, 'maxVarDist': 15, 'maxGOF': 30, 'rlen': 150, 'minGoodQualBases': 20, 'refCallBlockSize': 1000, 'countOnlyExactIndelMatches': 0, 'longHaps': 0, 'HLATyping': 0, 'filterReadPairsWithSmallInserts': 1, 'minBaseQual': 20, 'getVariantsFromBAMs': 1, 'genSNPs': 1, 'assemble': 0, 'assemblerKmerSize': 15, 'minVarFreq': 0.05, 'alignScoreFile': '', 'verbosity': 2, 'sourceFile': None, 'compressReads': 0, 'rmsmqThreshold': 40, 'filteredReadsFrac': 0.7, 'outputRefCalls': 0, 'badReadsThreshold': 15, 'hapScoreThreshold': 4, 'regions': None, 'sbThreshold': 0.001, 'output': '/data/TCGA-A2-A0YC/platypus_out.vcf', 'assembleBrokenPairs': 0, 'mergeClusteredVariants': 1, 'maxGenotypes': 1275, 'nInd': 1}
##filter="MQ > 50 & TC > 100 & QUAL > 2900"
##INFO=<ID=FR,Number=.,Type=Float,Description="Estimated population frequency of variant">
##INFO=<ID=MMLQ,Number=1,Type=Float,Description="Median minimum base quality for bases around variant">
##INFO=<ID=TCR,Number=1,Type=Integer,Description="Total reverse strand coverage at this locus">
##INFO=<ID=HP,Number=1,Type=Integer,Description="Homopolymer run length around variant locus">
##INFO=<ID=WE,Number=1,Type=Integer,Description="End position of calling window">
##INFO=<ID=Source,Number=.,Type=String,Description="Was this variant suggested by Playtypus, Assembler, or from a VCF?">
##INFO=<ID=FS,Number=.,Type=Float,Description="Fisher's exact test for strand bias (Phred scale)">
##INFO=<ID=WS,Number=1,Type=Integer,Description="Starting position of calling window">
##INFO=<ID=PP,Number=.,Type=Float,Description="Posterior probability (phred scaled) that this variant segregates">
##INFO=<ID=TR,Number=.,Type=Integer,Description="Total number of reads containing this variant">
##INFO=<ID=NF,Number=.,Type=Integer,Description="Total number of forward reads containing this variant">
##INFO=<ID=TCF,Number=1,Type=Integer,Description="Total forward strand coverage at this locus">
##INFO=<ID=NR,Number=.,Type=Integer,Description="Total number of reverse reads containing this variant">
##INFO=<ID=TC,Number=1,Type=Integer,Description="Total coverage at this locus">
##INFO=<ID=END,Number=.,Type=Integer,Description="End position of reference call block">
##INFO=<ID=MGOF,Number=.,Type=Integer,Description="Worst goodness-of-fit value reported across all samples">
##INFO=<ID=SbPval,Number=.,Type=Float,Description="Binomial P-value for strand bias test">
##INFO=<ID=START,Number=.,Type=Integer,Description="Start position of reference call block">
##INFO=<ID=ReadPosRankSum,Number=.,Type=Float,Description="Mann-Whitney Rank sum test for difference between in positions of variants in reads from ref and alt">
##INFO=<ID=MQ,Number=.,Type=Float,Description="Root mean square of mapping qualities of reads at the variant position">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant-quality/read-depth for this variant">
##INFO=<ID=SC,Number=1,Type=String,Description="Genomic sequence 10 bases either side of variant position">
##INFO=<ID=BRF,Number=1,Type=Float,Description="Fraction of reads around this variant that failed filters">
##INFO=<ID=HapScore,Number=.,Type=Integer,Description="Haplotype score measuring the number of haplotypes the variant is segregating into in a window">
##INFO=<ID=Size,Number=.,Type=Integer,Description="Size of reference call block">
##FILTER=<ID=GOF,Description="Variant fails goodness-of-fit test.">
##FILTER=<ID=badReads,Description="Variant supported only by reads with low quality bases close to variant position, and not present on both strands.">
##FILTER=<ID=alleleBias,Description="Variant frequency is lower than expected for het">
##FILTER=<ID=hp10,Description="Flanking sequence contains homopolymer of length 10 or greater">
##FILTER=<ID=Q20,Description="Variant quality is below 20.">
##FILTER=<ID=HapScore,Description="Too many haplotypes are supported by the data in this region.">
##FILTER=<ID=MQ,Description="Root-mean-square mapping quality across calling region is low.">
##FILTER=<ID=strandBias,Description="Variant fails strand-bias filter">
##FILTER=<ID=SC,Description="Variants fail sequence-context filter. Surrounding sequence is low-complexity">
##FILTER=<ID=QualDepth,Description="Variant quality/Read depth ratio is low.">
##FILTER=<ID=REFCALL,Description="This line represents a homozygous reference call">
##FILTER=<ID=QD,Description="Variants fail quality/depth filter.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Unphased genotypes">
##FORMAT=<ID=GQ,Number=.,Type=Integer,Description="Genotype quality as phred score">
##FORMAT=<ID=GOF,Number=.,Type=Float,Description="Goodness of fit value">
##FORMAT=<ID=NR,Number=.,Type=Integer,Description="Number of reads covering variant location in this sample">
##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype log10-likelihoods for AA,AB and BB genotypes, where A = ref and B = variant. Only applicable for bi-allelic sites">
##FORMAT=<ID=NV,Number=.,Type=Integer,Description="Number of reads containing variant in this sample">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
1	1158631	.	A	G	2965	PASS	BRF=0.16;FR=1.0000;HP=1;HapScore=1;MGOF=3;MMLQ=33;MQ=59.75;NF=89;NR=67;PP=2965;QD=20;SC=CACTTTCCTCATCCACTTTGA;SbPval=0.58;Source=Platypus;TC=160;TCF=90;TCR=70;TR=156;WE=1158639;WS=1158621	GT:GL:GOF:GQ:NR:NV	1/1:-300.0,-43.88,0.0:3:99:160:156
1	6219287	.	TCACACA	TCACA,T	2997	PASS	BRF=0.35;FR=0.5000,0.5000;HP=1;HapScore=1;MGOF=6;MMLQ=23;MQ=51.91;NF=108,108;NR=0,0;PP=2997,2652;QD=20;SC=TGAGACTCCATCACACACACA;SbPval=1.0;Source=Platypus;TC=172;TCF=170;TCR=2;TR=108,108;WE=6219302;WS=6219277	GT:GL:GOF:GQ:NR:NV	1/2:-1,-1,-1:6:99:172,172:108,108
1	12921332	.	TG	CA	2944	PASS	BRF=0.32;FR=0.5000;HP=1;HapScore=1;MGOF=7;MMLQ=35;MQ=50.57;NF=35;NR=52;PP=2944;QD=20;SC=TGGCCTGAGCTGCTGCTCCCA;SbPval=0.31;Source=Platypus;TC=198;TCF=70;TCR=128;TR=87;WE=12921341;WS=12921322	GT:GL:GOF:GQ:NR:NV	1/0:-300.0,0.0,-300.0:7:99:198:87
1	13173016	.	A	G	2965	PASS	BRF=0.12;FR=1.0000;HP=1;HapScore=1;MGOF=3;MMLQ=35;MQ=58.87;NF=53;NR=79;PP=2965;QD=20;SC=CTCCATGAACATCAGAGGGGA;SbPval=0.5;Source=Platypus;TC=133;TCF=53;TCR=80;TR=132;WE=13173024;WS=13173006	GT:GL:GOF:GQ:NR:NV	1/1:-300.0,-36.73,0.0:3:99:133:132
2	11053740	.	C	T	2965	PASS	BRF=0.09;FR=1.0000;HP=1;HapScore=1;MGOF=3;MMLQ=33;MQ=59.84;NF=53;NR=54;PP=2965;QD=20;SC=GTGGTGTCATCGCCATCGCCC;SbPval=0.49;Source=Platypus;TC=111;TCF=53;TCR=58;TR=107;WE=11053748;WS=11053730	GT:GL:GOF:GQ:NR:NV	1/1:-300.0,-29.78,0.0:3:99:111:107