Understand BCF (2)

BCFformat is explained at the top of the output: look no further… after 3 hours of googling.

##fileformat=VCFv4.1
##samtoolsVersion=0.1.17 (r973:277)
##INFO=<ID=DP,Number=1,Type=Integer,Description=”Raw read depth”>
##INFO=<ID=DP4,Number=4,Type=Integer,Description=”# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases”>
##INFO=<ID=MQ,Number=1,Type=Integer,Description=”Root-mean-square mapping quality of covering reads”>
##INFO=<ID=FQ,Number=1,Type=Float,Description=”Phred probability of all samples being the same”>
##INFO=HWE)”>
##INFO=HWE assumption)”>
##INFO=<ID=G3,Number=3,Type=Float,Description=”ML estimate of genotype frequencies”>
##INFO=HWE,Number=1,Type=Float,Description=”Chi^2 based HWE test P-value based on G3″>
##INFO=likelihoods with and without the constraint”>
##INFO=<ID=UGT,Number=1,Type=String,Description=”The most probable unconstrained genotype configuration in the trio”>
##INFO=<ID=CGT,Number=1,Type=String,Description=”The most probable constrained genotype configuration in the trio”>
##INFO=baseQ bias, mapQ bias and tail distance bias”>
##INFO=<ID=INDEL,Number=0,Type=Flag,Description=”Indicates that the variant is an INDEL.”>
##INFO=nonRef allele frequency in group1 samples being larger (,smaller) than in group2.”>
##INFO=group1 and group2 samples.”>
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=”Phred scaled PCHI2.”>
##INFO=<ID=PR,Number=1,Type=Integer,Description=”# permutations yielding a smaller PCHI2.”>
##INFO=<ID=VDB,Number=1,Type=Float,Description=”Variant Distance Bias”>
##FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”>
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=”Genotype Quality”>
##FORMAT=<ID=GL,Number=3,Type=Float,Description=”Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)”>
##FORMAT=<ID=DP,Number=1,Type=Integer,Description=”# high-quality bases”>
##FORMAT=<ID=SP,Number=1,Type=Integer,Description=”Phred-scaled strand bias P-value”>
##FORMAT=Phred-scaled genotype likelihoods”>

VCF (Variant Call Format) version 4.1 (personal note)

As with the INFO field, there are several common, reserved keywords that are standards across the community:

• GT : genotype, encoded as allele values separated by either of ”/” or “|”. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on.
• For diploid calls examples could be 0/1, 1|0, or 1/2, etc.
• For haploid calls, e.g. on Y, male non-pseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1.
• If a call cannot be made for a sample at a given locus, ”.” should be specified for each missing allele in the GT field (for example “./.” for a diploid genotype and “.” for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes):
  • / : genotype unphased
  • | : genotype phased
• DP : read depth at this position for this sample (Integer)
• FT : sample genotype filter indicating if this genotype was “called” (similar in concept to the FILTER field). Again, use PASS to indicate that all filters have been passed, a semi-colon separated list of codes for filters that fail, or ”.” to indicate that filters have not been applied. These values should be described in the meta-information in the same way as FILTERs (String, no white-space or semi-colons permitted)
• GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,… are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j.  In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc.  For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Numeric)
• GLE : genotype likelihoods of heterogeneous ploidy, used in presence of uncertain copy number. For example: GLE=0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53 (String)
• PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)
• GP : the phred-scaled genotype posterior probabilities (and otherwise defined precisely as the GL field); intended to store imputed genotype probabilities (Numeric)
• GQ : conditional genotype quality, encoded as a phred quality -10log_10p(genotype call is wrong, conditioned on the site’s being variant) (Numeric)
• HQ : haplotype qualities, two comma separated phred qualities (Numeric)
• PS : phase set.  A phase set is defined as a set of phased genotypes to which this genotype belongs.  Phased genotypes for an individual that are on the same chromosome and have the same PS value are in the same phased set.  A phase set specifies multi-marker haplotypes for the phased genotypes in the set.  All phased genotypes that do not contain a PS subfield are assumed to belong to the same phased set.  If the genotype in the GT field is unphased, the corresponding PS field is ignored.  The recommended convention is to use the position of the first variant in the set as the PS identifier (although this is not required). (Non-negative 32-bit Integer)
• PQ : phasing quality, the phred-scaled probability that alleles are ordered incorrectly in a heterozygote (against all other members in the phase set).  We note that we have not yet included the specific measure for precisely defining “phasing quality”; our intention for now is simply to reserve the PQ tag for future use as a measure of phasing quality. (Numeric)
• EC : comma separated list of expected alternate allele counts for each alternate allele in the same order as listed in the ALT field (typically used in association analyses) (Numeric)

Understand bcftools 1

Program: bcftools (Tools for data in the VCF/BCF formats)
Version: 0.1.17-dev (r973:277)
Usage:   bcftools

Command: view      print, extract, convert and call SNPs from BCF
index     index BCF
cat       concatenate BCFs
ld        compute all-pair r^2
ldpair    compute r^2 between requested pairs

 

Usage: bcftools view [options] [reg]

Input/output options:

-A        keep all possible alternate alleles at variant sites
-b        output BCF instead of VCF
-D FILE   sequence dictionary for VCF->BCF conversion [null]
-F        PL generated by r921 or before (which generate old ordering)
-G        suppress all individual genotype information
-l FILE   list of sites (chr pos) or regions (BED) to output [all sites]
-L        calculate LD for adjacent sites
-N        skip sites where REF is not A/C/G/T
-Q        output the QCALL likelihood format
-s FILE   list of samples to use [all samples]
-S        input is VCF
-u        uncompressed BCF output (force -b)

Consensus/variant calling options:

-c        SNP calling (force -e)
-d FLOAT  skip loci where less than FLOAT fraction of samples covered [0]
-e        likelihood based analyses
-g        call genotypes at variant sites (force -c)
-i FLOAT  indel-to-substitution ratio [-1]
-I        skip indels
-p FLOAT  variant if P(ref|D)
-P STR    type of prior: full, cond2, flat [full]
-t FLOAT  scaled substitution mutation rate [0.001]
-T STR    constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]
-v        output potential variant sites only (force -c)

Contrast calling and association test options:

-1 INT    number of group-1 samples [0]
-C FLOAT  posterior constrast for LRT
-U INT    number of permutations for association testing (effective with -1) [0]
-X FLOAT  only perform permutations for P(chi^2)

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