[File Format] VCF format

* 1000 genome proejct
http://www.1000genomes.org/wiki/Analysis/variant-call-format

• AA    ancestral allele
• AC    allele count in genotypes, for each ALT allele, in the same order as listed
• AF    allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes
• AN    total number of alleles in called genotypes
• BQ    RMS base quality at this position
• CIGAR    cigar string describing how to align an alternate allele to the reference allele
• DB    dbSNP membership
• DP    combined depth across samples, e.g. DP=154
• END    end position of the variant described in this record (esp. for CNVs)
• H2    membership in hapmap2
• MQ    RMS mapping quality, e.g. MQ=52
• MQ0    Number of MAPQ == 0 reads covering this record
• NS    Number of samples with data
• SB    strand bias at this position
• SOMATIC    indicates that the record is a somatic mutation, for cancer genomics
• VALIDATED    validated by follow-up experiment

* samtools mpileup
http://samtools.sourceforge.net/mpileup.shtml

Tag Description

• I16
  • 1 #reference Q13 bases on the forward strand 2 #reference Q13 bases on the reverse strand
  • 3 #non-ref Q13 bases on the forward strand 4 #non-ref Q13 bases on the reverse strand
  • 5 sum of reference base qualities 6 sum of squares of reference base qualities
  • 7 sum of non-ref base qualities 8 sum of squares of non-ref base qualities
  • 9 sum of ref mapping qualities 10 sum of squares of ref mapping qualities
  • 11 sum of non-ref mapping qualities 12 sum of squares of non-ref mapping qualities
  • 13 sum of tail distance for ref bases 14 sum of squares of tail distance for ref bases
  • 15 sum of tail distance for non-ref bases 16 sum of squares of tail distance for non-ref
• INDEL    Indicating the variant is an INDEL.
• DP    The number of reads covering or bridging POS.
• DP4    Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling. Sum can be smaller than DP because low-quality bases are not counted.
• PV4    P-values for 1) strand bias (exact test); 2) baseQ bias (t-test); 3) mapQ bias (t); 4) tail distance bias (t)
• FQ    Consensus quality. If positive, FQ equals the phred-scaled probability of there being two or more different alleles. If negative, FQ equals the minus phred-scaled probability of all chromosomes being identical. Notably, given one sample, FQ is positive at hets and negative at homs.
• AF1    EM estimate of the site allele frequency of the strongest non-reference allele.
• CI95    Equal-tail (Bayesian) credible interval of the site allele frequency at the 95% level.
• PC2    Phred-scaled probability of the alternate allele frequency of group1 samples being larger (,smaller) than of group2 samples.
• PCHI2    Posterior weighted chi^2 P-value between group1 and group2 samples. This P-value is conservative.
• QCHI2    Phred-scaled PCHI2
• RP    Number of permutations yeilding a smaller PCHI2

 
Specifications for VCF format are different in Info field.