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##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
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##contig=<ID=GL000214.1,length=137718>
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##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
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##contig=<ID=GL000216.1,length=172294>
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##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
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##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##SAMPLE=<ID=BriGibBld,Genomes=Germline>
##PEDIGREE=<Derived=BriGibFFPE,Original=BriGibBld>
##FILTER=<ID=Bias,Description="Strand Bias">
##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">
##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">
##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">
##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">
##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">
##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">
##FILTER=<ID=LowAlleleDepth,Description="Low depth per allele frequency along with poor depth, quality, mapping quality and read mismatches.">
##FILTER=<ID=LowFreqQuality,Description="Low frequency read with poor quality and p-value (SSF).">
##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">
##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">
##FILTER=<ID=NM4.25,Description="Mean mismatches in reads >= 4.25, thus likely false positive">
##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">
##FILTER=<ID=P0.9,Description="Not significant with p-value > 0.9">
##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
##FILTER=<ID=REJECT,Description="Not somatic due to normal call frequency or phred likelihoods: tumor: 35, normal 35.">
##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
##FILTER=<ID=SpvFreq,Description="High frequency (tumor FREQ > 0.35) and low p-value for somatic (SPV < 0.05)">
##FILTER=<ID=artifact_in_normal,Description="artifact_in_normal">
##FILTER=<ID=bPcr,Description="Variant allele shows a bias towards one PCR template strand.">
##FILTER=<ID=bSeq,Description="Variant allele shows a bias towards one sequencing strand.">
##FILTER=<ID=base_quality,Description="alt median base quality">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=contamination,Description="contamination">
##FILTER=<ID=d5,Description="Total Depth < 5">
##FILTER=<ID=duplicate_evidence,Description="evidence for alt allele is overrepresented by apparent duplicates">
##FILTER=<ID=f0.1,Description="Allele frequency < 0.1">
##FILTER=<ID=fragment_length,Description="abs(ref - alt) median fragment length">
##FILTER=<ID=germline_risk,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
##FILTER=<ID=mapping_quality,Description="ref - alt median mapping quality">
##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
##FILTER=<ID=read_position,Description="median distance of alt variants from end of reads">
##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
##FILTER=<ID=str_contraction,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_artifact,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=t_lod,Description="Tumor does not meet likelihood threshold">
##FILTER=<ID=v3,Description="Var Depth < 3">
##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=ACGTNacgtnMINUS,Number=10,Type=Integer,Description="The first five numbers correspond to the number of bases on forward reads found to be A, C, G, T, or N, while the last five numbers correspond to bases on reverse reads found to be a, c, g, t, or n on minus stranded PCR templates (only reads with a mapping quality greater or equal to 30, and bases with a base quality greater or equal to 13 were considered).">
##INFO=<ID=ACGTNacgtnPLUS,Number=10,Type=Integer,Description="The first five numbers correspond to the number of bases on forward reads found to be A, C, G, T, or N, while the last five numbers correspond to bases on reverse reads found to be a, c, g, t, or n on plus stranded PCR templates (only reads with a mapping quality greater or equal to 30, and bases with a base quality greater or equal to 13 were considered).">
##INFO=<ID=AF,Number=1,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=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
##INFO=<ID=CALLERS,Number=.,Type=String,Description="Individual caller support">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DKFZBias,Number=.,Type=String,Description="Bias estimation based on unequal read support from DKFZBiasFilterVariant Depth">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
##INFO=<ID=IN_PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">
##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">
##INFO=<ID=NLOD,Number=1,Type=Float,Description="Normal LOD score">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=N_ART_LOD,Number=1,Type=Float,Description="log odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=POP_AF,Number=1,Type=Float,Description="population allele frequencies of alt alleles">
##INFO=<ID=P_GERMLINE,Number=1,Type=Float,Description="Posterior probability for alt allele to be germline variants">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">
##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">
##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
##INFO=<ID=SSC,Number=1,Type=Float,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">
##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
##INFO=<ID=TLOD,Number=1,Type=Float,Description="Tumor LOD score">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##INFO=<ID=ac_adj_exac_afr,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_AFR from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_adj_exac_amr,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_AMR from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_adj_exac_eas,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_EAS from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_adj_exac_fin,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_FIN from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_adj_exac_nfe,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_NFE from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_adj_exac_oth,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_OTH from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_adj_exac_sas,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_SAS from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=ac_exac_all,Number=1,Type=Float,Description="calculated by max of overlapping values in field AC_Adj from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz">
##INFO=<ID=af_1kg_afr,Number=1,Type=Float,Description="calculated by max of overlapping values in field AFR_AF from /data/projects/punim0010/local/share/bcbio/gemini_data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz">
##INFO=<ID=af_1kg_all,Number=1,Type=Float,Description="calculated by max of overlapping values in field AF from /data/projects/punim0010/local/share/bcbio/gemini_data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz">
##INFO=<ID=af_1kg_amr,Number=1,Type=Float,Description="calculated by max of overlapping values in field AMR_AF from /data/projects/punim0010/local/share/bcbio/gemini_data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz">
##INFO=<ID=af_1kg_eas,Number=1,Type=Float,Description="calculated by max of overlapping values in field EAS_AF from /data/projects/punim0010/local/share/bcbio/gemini_data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz">
##INFO=<ID=af_1kg_eur,Number=1,Type=Float,Description="calculated by max of overlapping values in field EUR_AF from /data/projects/punim0010/local/share/bcbio/gemini_data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz">
##INFO=<ID=af_1kg_sas,Number=1,Type=Float,Description="calculated by max of overlapping values in field SAS_AF from /data/projects/punim0010/local/share/bcbio/gemini_data/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.tidy.vcf.gz">
##INFO=<ID=af_adj_exac_afr,Number=1,Type=Float,Description="calculated field: af_adj_exac_afr">
##INFO=<ID=af_adj_exac_amr,Number=1,Type=Float,Description="calculated field: af_adj_exac_amr">
##INFO=<ID=af_adj_exac_eas,Number=1,Type=Float,Description="calculated field: af_adj_exac_eas">
##INFO=<ID=af_adj_exac_fin,Number=1,Type=Float,Description="calculated field: af_adj_exac_fin">
##INFO=<ID=af_adj_exac_nfe,Number=1,Type=Float,Description="calculated field: af_adj_exac_nfe">
##INFO=<ID=af_adj_exac_oth,Number=1,Type=Float,Description="calculated field: af_adj_exac_oth">
##INFO=<ID=af_adj_exac_sas,Number=1,Type=Float,Description="calculated field: af_adj_exac_sas">
##INFO=<ID=af_esp_aa,Number=1,Type=Float,Description="calculated by lua:ratio(vals) of overlapping values in field AA_AC from /data/projects/punim0010/local/share/bcbio/gemini_data/ESP6500SI.all.snps_indels.tidy.v2.vcf.gz">
##INFO=<ID=af_esp_all,Number=1,Type=Float,Description="calculated by lua:ratio(vals) of overlapping values in field TAC from /data/projects/punim0010/local/share/bcbio/gemini_data/ESP6500SI.all.snps_indels.tidy.v2.vcf.gz">
##INFO=<ID=af_esp_ea,Number=1,Type=Float,Description="calculated by lua:ratio(vals) of overlapping values in field EA_AC from /data/projects/punim0010/local/share/bcbio/gemini_data/ESP6500SI.all.snps_indels.tidy.v2.vcf.gz">
##INFO=<ID=af_exac_all,Number=1,Type=Float,Description="calculated field: af_exac_all">
##INFO=<ID=an_adj_exac_afr,Number=1,Type=Integer,Description="African/African American Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_adj_exac_amr,Number=1,Type=Integer,Description="American Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_adj_exac_eas,Number=1,Type=Integer,Description="East Asian Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_adj_exac_fin,Number=1,Type=Integer,Description="Finnish Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_adj_exac_nfe,Number=1,Type=Integer,Description="Non-Finnish European Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_adj_exac_oth,Number=1,Type=Integer,Description="Other Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_adj_exac_sas,Number=1,Type=Integer,Description="South Asian Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=an_exac_all,Number=1,Type=Integer,Description="Adjusted Chromosome Count (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=clinvar_disease_name,Number=.,Type=String,Description="Variant disease name (from /data/projects/punim0010/local/share/bcbio/gemini_data/clinvar_20170130.tidy.vcf.gz)">
##INFO=<ID=clinvar_pathogenic,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 7 - histocompatibility, 255 - other (from /data/projects/punim0010/local/share/bcbio/gemini_data/clinvar_20170130.tidy.vcf.gz)">
##INFO=<ID=clinvar_sig,Number=.,Type=String,Description="calculated field: clinvar_sig">
##INFO=<ID=common_pathogenic,Number=0,Type=Flag,Description="calculated field: common_pathogenic">
##INFO=<ID=cosmic_ids,Number=.,Type=String,Description="calculated by uniq of overlapping values in field ID from /data/projects/punim0010/local/share/bcbio/gemini_data/cosmic-v68-GRCh37.tidy.vcf.gz">
##INFO=<ID=cpg_island,Number=0,Type=Flag,Description="calculated by flag of overlapping values in column 2 from /data/projects/punim0010/local/share/bcbio/gemini_data/hg19.CpG.bed.gz">
##INFO=<ID=cse-hiseq,Number=0,Type=Flag,Description="calculated by flag of overlapping values in column 2 from /data/projects/punim0010/local/share/bcbio/gemini_data/cse-hiseq-8_4-2013-02-20.bed.gz">
##INFO=<ID=dgv,Number=.,Type=String,Description="calculated by uniq of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/hg19.dgv.bed.gz">
##INFO=<ID=encode_consensus_gm12878,Number=.,Type=String,Description="calculated by concat of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/encode.6celltypes.consensus.bedg.gz">
##INFO=<ID=encode_consensus_h1hesc,Number=.,Type=String,Description="calculated by concat of overlapping values in column 5 from /data/projects/punim0010/local/share/bcbio/gemini_data/encode.6celltypes.consensus.bedg.gz">
##INFO=<ID=encode_consensus_helas3,Number=.,Type=String,Description="calculated by concat of overlapping values in column 6 from /data/projects/punim0010/local/share/bcbio/gemini_data/encode.6celltypes.consensus.bedg.gz">
##INFO=<ID=encode_consensus_hepg2,Number=.,Type=String,Description="calculated by concat of overlapping values in column 7 from /data/projects/punim0010/local/share/bcbio/gemini_data/encode.6celltypes.consensus.bedg.gz">
##INFO=<ID=encode_consensus_huvec,Number=.,Type=String,Description="calculated by concat of overlapping values in column 8 from /data/projects/punim0010/local/share/bcbio/gemini_data/encode.6celltypes.consensus.bedg.gz">
##INFO=<ID=encode_consensus_k562,Number=.,Type=String,Description="calculated by concat of overlapping values in column 9 from /data/projects/punim0010/local/share/bcbio/gemini_data/encode.6celltypes.consensus.bedg.gz">
##INFO=<ID=fitcons,Number=1,Type=Float,Description="calculated by mean of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/hg19_fitcons_fc-i6-0_V1-01.bed.gz">
##INFO=<ID=gerp_elements,Number=1,Type=Float,Description="calculated by mean of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/hg19.gerp.elements.bed.gz">
##INFO=<ID=gwas_pubmed_trait,Number=.,Type=String,Description="calculated by uniq of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/hg19.gwas.bed.gz">
##INFO=<ID=hapmap1,Number=1,Type=Float,Description="calculated by mean of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/genetic_map_HapMapII_GRCh37.gz">
##INFO=<ID=hapmap2,Number=1,Type=Float,Description="calculated by mean of overlapping values in column 5 from /data/projects/punim0010/local/share/bcbio/gemini_data/genetic_map_HapMapII_GRCh37.gz">
##INFO=<ID=max_aaf_all,Number=1,Type=Float,Description="calculated field: max_aaf_all">
##INFO=<ID=num_exac_Het,Number=1,Type=Integer,Description="Adjusted Heterozygous Counts (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=num_exac_Hom,Number=1,Type=Integer,Description="Adjusted Homozygous Counts (from /data/projects/punim0010/local/share/bcbio/gemini_data/ExAC.r0.3.sites.vep.tidy.vcf.gz)">
##INFO=<ID=rmsk,Number=.,Type=String,Description="calculated by uniq of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/hg19.rmsk.bed.gz">
##INFO=<ID=rs_ids,Number=.,Type=String,Description="calculated by concat of overlapping values in field ID from /data/projects/punim0010/local/share/bcbio/gemini_data/dbsnp.b147.20160601.tidy.vcf.gz">
##INFO=<ID=stam_mean,Number=1,Type=Float,Description="calculated by mean of overlapping values in column 5 from /data/projects/punim0010/local/share/bcbio/gemini_data/stam.125cells.dnaseI.hg19.bed.gz">
##INFO=<ID=stam_names,Number=.,Type=String,Description="calculated by uniq of overlapping values in column 6 from /data/projects/punim0010/local/share/bcbio/gemini_data/stam.125cells.dnaseI.hg19.bed.gz">
##INFO=<ID=tfbs,Number=.,Type=String,Description="calculated by uniq of overlapping values in column 4 from /data/projects/punim0010/local/share/bcbio/gemini_data/wgEncodeRegTfbsClusteredV2.cell_count.20130213.bed.gz">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">
##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">
##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
##FORMAT=<ID=FREQ,Number=1,Type=Float,Description="Variant allele frequency">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">
##FORMAT=<ID=MMQ,Number=1,Type=Float,Description="median mapping quality">
##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">
##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">
##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
##FORMAT=<ID=PID,Number=1,Type=String,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=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">
##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">
##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">
##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">
##FORMAT=<ID=RD,Number=.,Type=Integer,Description="Reference forward, reverse reads">
##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">
##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">
##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">
##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls  --output /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/bcbiotx/tmpcSVwJH/batch1-1_0_16151943.vcf.gz --variant /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/bcbiotx/tmpcSVwJH/batch1-1_0_16151943-raw.vcf.gz  --tumor_lod 5.3 --normal_artifact_lod 0.0 --max_germline_posterior 0.025 --maxAltAllelesThreshold 1 --minMedianMappingQuality 30 --minMedianBaseQuality 20 --maxMedianFragmentLengthDifference 10000 --minMedianReadPosition 5 --maxEventsInHaplotype 2 --strandArtifactPosteriorProbability 0.99 --strandArtifactAlleleFraction 0.01 --uniqueAltReadCount 0 --dontTrimActiveRegions false --maxDiscARExtension 25 --maxGGAARExtension 300 --paddingAroundIndels 150 --paddingAroundSNPs 20 --kmerSize 10 --kmerSize 25 --dontIncreaseKmerSizesForCycles false --allowNonUniqueKmersInRef false --numPruningSamples 1 --recoverDanglingHeads false --doNotRecoverDanglingBranches false --minDanglingBranchLength 4 --consensus false --maxNumHaplotypesInPopulation 128 --errorCorrectKmers false --minPruning 2 --debugGraphTransformations false --kmerLengthForReadErrorCorrection 25 --minObservationsForKmerToBeSolid 20 --likelihoodCalculationEngine PairHMM --base_quality_score_threshold 18 --gcpHMM 10 --pair_hmm_implementation FASTEST_AVAILABLE --pcr_indel_model CONSERVATIVE --phredScaledGlobalReadMismappingRate 45 --nativePairHmmThreads 4 --useDoublePrecision false --debug false --useFilteredReadsForAnnotations false --emitRefConfidence NONE --bamWriterType CALLED_HAPLOTYPES --disableOptimizations false --justDetermineActiveRegions false --dontGenotype false --dontUseSoftClippedBases false --captureAssemblyFailureBAM false --errorCorrectReads false --doNotRunPhysicalPhasing false --min_base_quality_score 10 --useNewAFCalculator false --annotateNDA false --heterozygosity 0.001 --indel_heterozygosity 1.25E-4 --heterozygosity_stdev 0.01 --standard_min_confidence_threshold_for_calling 10.0 --max_alternate_alleles 6 --max_genotype_count 1024 --sample_ploidy 2 --genotyping_mode DISCOVERY --contamination_fraction_to_filter 0.0 --output_mode EMIT_VARIANTS_ONLY --allSitePLs false --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --interval_merging_rule ALL --readValidationStringency SILENT --secondsBetweenProgressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --createOutputBamMD5 false --createOutputVariantIndex true --createOutputVariantMD5 false --lenient false --addOutputSAMProgramRecord true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disableBamIndexCaching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --gcs_max_retries 20 --disableToolDefaultReadFilters false",Version=4.beta.4,Date="September 18, 2017 3:15:59 PM AEST">
##Mutect Version=2.1-beta
##SnpEffCmd="SnpEff  -cancer -i vcf -o vcf -csvStats /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1-effects-stats.csv -s /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1-effects-stats.html GRCh37.75 /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1.vcf.gz "
##SnpEffVersion="4.3i (build 2016-12-15 22:33), by Pablo Cingolani"
##bcftools_annotateCommand=annotate --set-id +%INFO/rs_ids -o /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/bcbiotx/tmpgXBf2A/batch1-1_0_16151943.vcf.gz -O z; Date=Sun Sep 17 09:57:35 2017
##bcftools_annotateVersion=1.5+htslib-1.5
##bcftools_filterCommand=filter -i 'QUAL >= 0'; Date=Sun Sep 17 09:57:28 2017
##bcftools_filterVersion=1.5+htslib-1.5
##bcftools_viewCommand=view -f PASS,. -O z -o /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/bcbiotx/tmpjSPYhS/batch1-ensemble-work/txtmp6440159648747552230/vardict-batch1-effects-annotated-damage-ann-nofilter.vcf.gz /data/projects/punim0010/projects/Grimmond_Patients/brigibFFPE/work/vardict/batch1-effects-annotated-damage-ann.vcf.gz; Date=Tue Sep 19 18:31:21 2017
##bcftools_viewVersion=1.5+htslib-1.5
##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
##normal_sample=BriGibBld
##reference=file:///data/projects/punim0010/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa
##source=VarScan2
##tumor_sample=BriGibFFPE
##bcftools_viewCommand=view -r 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y batch1-ensemble-annotated.vcf.gz; Date=Wed Sep 20 16:30:20 2017
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	BriGibFFPE	BriGibBld
1	16234	.	T	C	210	PASS	ACGTNacgtnMINUS=0,12,0,40,0,0,15,0,8,0;ACGTNacgtnPLUS=0,7,0,36,0,0,13,0,4,0;ANN=C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000456328|processed_transcript||n.*1825T>C|||||1825|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000515242|transcribed_unprocessed_pseudogene||n.*1822T>C|||||1822|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000518655|transcribed_unprocessed_pseudogene||n.*1825T>C|||||1825|,C|downstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|transcript|ENST00000450305|transcribed_unprocessed_pseudogene||n.*2564T>C|||||2564|,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000438504|unprocessed_pseudogene|8/11|n.1098-287A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000541675|unprocessed_pseudogene|7/8|n.880+620A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000423562|unprocessed_pseudogene|7/9|n.982-287A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000488147|unprocessed_pseudogene|8/10|n.1068-287A>G||||||,C|intron_variant|MODIFIER|WASH7P|ENSG00000227232|transcript|ENST00000538476|unprocessed_pseudogene|9/12|n.1303-287A>G||||||;CALLERS=vardict,varscan,mutect2;LSEQ=CCATGCTCTGACAGTCTCAG;MSI=2;MSILEN=1;RSEQ=TGCACACACGAGCCAGCAGA;SAMPLE=BriGibFFPE;SHIFT3=0;SOMATIC;SOR=inf;SSF=0;STATUS=StrongSomatic;TYPE=SNV;fitcons=0.2558;encode_consensus_gm12878=T;encode_consensus_h1hesc=CTCF;encode_consensus_helas3=T;encode_consensus_hepg2=T;encode_consensus_huvec=CTCF;encode_consensus_k562=CTCF;dgv=CopyNumber;tfbs=CTCF;hapmap1=2.9818;hapmap2=0;stam_mean=18.7689;stam_names=CD34,CMK,Fibrobl,HFF,SK_N_MC	GT:AD:ADJAF:AF:ALD:BIAS:DP:HIAF:MQ:NM:ODDRATIO:PMEAN:PSTD:QSTD:QUAL:RD:SBF:SN:VD	0/1:213,54:0:0.2022:21,33:2,2:267:0.2087:45.7:1.4:12.1955:31.7:1:1:36.5:189,24:0:53:54	0/0:97,0:0:0:0,0:2,0:98:1:37.3:0.8:0:38.7:1:1:35.3:70,27:1:12.857:0