vcf.xml

<?xml version="1.0" encoding="UTF-8"?>
<vcf xmlns="http://www.umr915.univ-nantes.fr/vcf/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/">
  <header>
    <format>VCFv3.3</format>
    <formats>
      <format>
        <id>GT</id>
        <desc>Genotype</desc>
        <type>String</type>
        <count>1</count>
      </format>
      <format>
        <id>GQ</id>
        <desc>Genotype Quality</desc>
        <type>Float</type>
        <count>1</count>
      </format>
      <format>
        <id>DP</id>
        <desc>Read Depth (only filtered reads used for calling)</desc>
        <type>Integer</type>
        <count>1</count>
      </format>
      <format>
        <id>GL</id>
        <desc>Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic</desc>
        <type>Float</type>
        <count>3</count>
      </format>
    </formats>
    <infos>
      <info>
        <id>AC</id>
        <desc>Allele count in genotypes, for each ALT allele, in the same order as listed</desc>
        <type>Integer</type>
        <count>1</count>
      </info>
      <info>
        <id>HRun</id>
        <desc>Largest Contiguous Homopolymer Run of Variant Allele In Either Direction</desc>
        <type>Integer</type>
        <count>1</count>
      </info>
      <info>
        <id>AB</id>
        <desc>Allele Balance for hets (ref/(ref+alt))</desc>
        <type>Float</type>
        <count>1</count>
      </info>
      <info>
        <id>Dels</id>
        <desc>Fraction of Reads Containing Spanning Deletions</desc>
        <type>Float</type>
        <count>1</count>
      </info>
      <info>
        <id>DP</id>
        <desc>Total Depth</desc>
        <type>Integer</type>
        <count>1</count>
      </info>
      <info>
        <id>QD</id>
        <desc>Variant Confidence/Quality by Depth</desc>
        <type>Float</type>
        <count>1</count>
      </info>
      <info>
        <id>AF</id>
        <desc>Allele Frequency</desc>
        <type>Float</type>
        <count>1</count>
      </info>
      <info>
        <id>MQ0</id>
        <desc>Total Mapping Quality Zero Reads</desc>
        <type>Integer</type>
        <count>1</count>
      </info>
      <info>
        <id>MQ</id>
        <desc>RMS Mapping Quality</desc>
        <type>Float</type>
        <count>1</count>
      </info>
      <info>
        <id>SB</id>
        <desc>Strand Bias</desc>
        <type>Float</type>
        <count>1</count>
      </info>
      <info>
        <id>AN</id>
        <desc>Total number of alleles in called genotypes</desc>
        <type>Integer</type>
        <count>1</count>
      </info>
    </infos>
    <filters/>
    <meta>
      <property>##UG_assume_single_sample_reads=null</property>
      <property>##UG_base_model=EMPIRICAL</property>
      <property>##UG_genotype=false</property>
      <property>##UG_genotype_model=JOINT_ESTIMATE</property>
      <property>##UG_heterozygosity=0.0010</property>
      <property>##UG_max_deletion_fraction=0.05</property>
      <property>##UG_max_mismatches_in_40bp_window=3</property>
      <property>##UG_min_base_quality_score=10</property>
      <property>##UG_min_confidence_threshold=50.0</property>
      <property>##UG_min_mapping_quality_score=10</property>
      <property>##UG_noSLOD=false</property>
      <property>##UG_output_all_callable_bases=false</property>
      <property>##UG_platform=SOLEXA</property>
      <property>##UG_poolSize=0</property>
      <property>##UG_use_reads_with_bad_mates=false</property>
      <property>##reference=chrN.fa</property>
      <property>##source=UnifiedGenotyper</property>
    </meta>
    <columns count="11">
      <column index="0">#CHROM</column>
      <column index="1">POS</column>
      <column index="2">ID</column>
      <column index="3">REF</column>
      <column index="4">ALT</column>
      <column index="5">QUAL</column>
      <column index="6">FILTER</column>
      <column index="7">INFO</column>
      <column index="8">FORMAT</column>
      <column index="9">chrN.markdup.bam</column>
      <column index="10">chrN.sorted.bam</column>
    </columns>
    <samples count="2">
      <sample index="0">chr.markdup.bam</sample>
      <sample index="1">chrN.sorted.bam</sample>
    </samples>
  </header>
  <body>
    <variant>
      <chromosome>chrN</chromosome>
      <position>109</position>
      <ref>A</ref>
      <alt>T</alt>
      <quality>94.5</quality>
      <info>
        <property name="AC">2</property>
        <property name="HRun">0</property>
        <property name="AB">0.67</property>
        <property name="Dels">0.00</property>
        <property name="DP">14</property>
        <property name="QD">6.75</property>
        <property name="AF">0.50</property>
        <property name="MQ0">4</property>
        <property name="MQ">19.70</property>
        <property name="SB">-64.74</property>
        <property name="AN">4</property>
      </info>
      <call index="0">
        <GT>0/1</GT>
        <DP>4</DP>
        <GL>-8.74,-2.21,-6.80</GL>
        <GQ>45.90</GQ>
      </call>
      <call index="1">
        <GT>0/1</GT>
        <DP>4</DP>
        <GL>-8.74,-2.21,-6.80</GL>
        <GQ>45.90</GQ>
      </call>
    </variant>
    <variant>
      <chromosome>chrN</chromosome>
      <position>578</position>
      <ref>G</ref>
      <alt>A</alt>
      <quality>120.87</quality>
      <info>
        <property name="AC">4</property>
        <property name="HRun">0</property>
        <property name="Dels">0.00</property>
        <property name="DP">4</property>
        <property name="QD">30.22</property>
        <property name="AF">1.00</property>
        <property name="MQ0">0</property>
        <property name="MQ">50.00</property>
        <property name="SB">-87.10</property>
        <property name="AN">4</property>
      </info>
      <call index="0">
        <GT>1/1</GT>
        <DP>2</DP>
        <GL>-8.92,-1.60,-1.00</GL>
        <GQ>6.02</GQ>
      </call>
      <call index="1">
        <GT>1/1</GT>
        <DP>2</DP>
    (...)
      </call>
    </variant>
  </body>
</vcf>