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What are EviCons? GenomicConsensus? Quiver? Plurality?
======================================================

**GenomicConsensus** is the current PacBio consensus and variant calling
suite. It contains a main driver program, `variantCaller`, which
provides two consensus/variant calling algorithms: **Arrow** and
**Quiver**. These algorithms can be run by calling
`variantCaller --algorithm=[arrow|quiver|plurality]` or by going
through the convenience wrapper scripts `quiver` and `arrow`.

**EviCons** was the previous generation PacBio variant caller (removed
:   in software release v1.3.1).

Separate packages called **ConsensusCore** and **ConsensusCore2** are
C++ libraries where all the computation behind Quiver and Arrow are
done, respectively. This is transparent to the user after installation.

What is Plurality?
==================

**Plurality** is a very simple variant calling algorithm: it stacks up
the aligned reads (alignment as produced by BLASR, or alternate mapping
tool), and for each column under a reference base, calls the most
abundant (i.e., the plurality) read base (or bases, or deletion) as the
consensus at that reference position.

Why is Plurality a weak algorithm?
==================================

Plurality does not perform any local realignment. This means it is
heavily biased by the alignment produced by the mapper (BLASR,
typically). It also means that it is insensitive at detecting indels.
Consider this example:

    Reference    AAAA
                 ----
      Aligned    A-AA
        reads    AA-A
                 -AAA
                 ----
    Plurality    AAAA
    consensus

Note here that every read has a deletion and the correct consensus call
would be "AAA", but due to the mapper's freedom in gap-placement at the
single-read level, the plurality sequence is "AAAA"---so the deletion is
missed. Local realignment, which plurality does not do, but which could
be considered as implicit in the Quiver algorithm, essentially pushes
the gaps here to the same column, thus identifying the deletion. While
plurality could be adjusted to use a simple "gap normalizing"
realignment, in practice noncognate extras (spurious non-homopolymer
base calls) in the midst of homopolymer runs pose challenges.

What is Quiver?
===============

**Quiver** is a more sophisticated algorithm that finds the maximum
quasi-likelihood template sequence given PacBio reads of the template.
PacBio reads are modeled using a conditional random field approach that
scores the quasi-likelihood of a read given a template sequence. In
addition to the base sequence of each read, Quiver uses several
additional *QV* covariates that the basecaller provides. Using these
covariates provides additional information about each read, allowing
more accurate consensus calls.

Quiver does not use the alignment provided by the mapper (BLASR,
typically), except for determining how to group reads together at a
macro level. It implicitly performs its own realignment, so it is highly
sensitive to all variant types, including indels---for example, it
resolves the example above with ease.

The name **Quiver** reflects a consensus-calling algorithm that is
QV-aware.

We use the lowercase "quiver" to denote the quiver *tool* in
GenomicConsensus, which applies the Quiver algorithm to mapped reads to
derive sequence consensus and variants.

Quiver is described in detail in the supplementary material to the [HGAP
paper](http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2474.html).

What is Arrow?
==============

Arrow is a newer model intended to supercede Quiver in the near future.
The key differences from Quiver are that it uses an HMM model instead of
a CRF, it computes true likelihoods, and it uses a smaller set of
covariates. We expect a whitepaper on Arrow to be available soon.

We use the lowercase "arrow" to denote the arrow *tool*, which applies
the Arrow algorithm to mapped reads to derive sequence consensus and
variants.

How do I run quiver/arrow?
==========================

For general instructions on installing and running, see the
[HowTo](./HowTo.rst) document.

What is the output from quiver/arrow?
=====================================

There are three output files from the GenomicConsensus tools:

1.  A consensus *FASTA* file containing the consensus sequence
2.  A consensus *FASTQ* file containing the consensus sequence with
    quality annotations
3.  A variants *GFF* file containing a filtered, annotated list of
    variants identified

It is important to note that the variants included in the output
variants GFF file are *filtered* by coverage and quality, so not all
variants that are apparent in comparing the reference to the consensus
FASTA output will correspond to variants in the output variants GFF
file.

To enable all output files, the following can be run (for example):

    % quiver -j16 aligned_reads.cmp.h5 -r ref.fa \
     -o consensus.fa                             \
     -o consensus.fq                             \
     -o variants.gff

The extension is used to determine the output file format.

What does it mean that quiver consensus is *de novo*?
=====================================================

Quiver's consensus is *de novo* in the sense that the reference and the
reference alignment are not used to inform the consensus output. Only
the reads factor into the determination of the consensus.

The only time the reference sequence is used to make consensus calls
-when the `--noEvidenceConsensusCall` flag is set to `reference` or
`lowercasereference` (the default)- is when there is no effective
coverage in a genomic window, so Quiver has no evidence for computing
consensus. One can set `--noEvidenceConsensusCall=nocall` to avoid using
the reference even in zero coverage regions.

What is the expected quiver accuracy?
=====================================

Quiver's expected accuracy is a function of coverage and chemistry. The
C2 chemistry (no longer available), P6-C4 and P4-C2 chemistries provide
the most accuracy. Nominal consensus accuracy levels are as follows:

  --------------------------------------------
  Coverage +  Expected consensus accuracy
              ------------------+------------+
              C2, P4-C2, P6-C4 | P5-C3
  ----------- --------------------------------
  10x         \> Q30 | \> Q30

  20x         \> Q40 | \> Q40

  40x         \> Q50 | \> Q45

  60-80x      \~ Q60 | \> Q55
  --------------------------------------------

The "Q" values referred to are Phred-scaled quality values:

$$q = -10 \log_{10} p_{error}$$

for instance, Q50 corresponds to a p\_error of 0.00001---an accuracy of
99.999%. These accuracy expectations are based on routine validations
performed on multiple bacterial genomes before each chemistry release.

What is the expected accuracy from arrow
========================================

arrow achieves similar accuracy to quiver. Numbers will be published
soon.

What are the residual errors after applying quiver?
===================================================

If there are errors remaining applying Quiver, they will almost
invariably be homopolymer run-length errors (insertions or deletions).

Does quiver/arrow need to know what sequencing chemistry was used?
==================================================================

At present, the Quiver model is trained per-chemistry, so it is very
important that Quiver knows the sequencing chemistries used.

If SMRT Analysis software was used to build the cmp.h5 or BAM input
file, the cmp.h5 will be loaded with information about the sequencing
chemistry used for each SMRT Cell, and GenomicConsensus will
automatically identify the right parameters to use.

If custom software was used to build the cmp.h5, or an override of
Quiver's autodetection is desired, then the chemistry or model must be
explicity entered. For example:

    % quiver -p P4-C2 ...
    % quiver -p P4-C2.AllQVsMergingByChannelModel ...

Can a mix of chemistries be used in a cmp.h5 file for quiver/arrow?
===================================================================

Yes! GenomicConsensus tools automatically see the chemistry *per-SMRT
Cell*, so it can figure out the right parameters for each read and model
them appropriately.

What chemistries and chemistry mixes are supported?
===================================================

For Quiver: all PacBio RS chemistries are supported. Chemistry mixtures
of P6-C4, P4-C2, P5-C3, and C2 are supported.

For Arrow: the RS chemistry P6-C4, and all PacBio Sequel chemistries are
supported. Mixes of these chemistries are supported.

What are the QVs that the Quiver model uses?
============================================

Quiver uses additional QV tracks provided by the basecaller. These QVs
may be looked at as little breadcrumbs that are left behind by the
basecaller to help identify positions where it was likely that errors of
a given type occurred. Formally, the QVs for a given read are vectors of
the same length as the number of bases called; the QVs used are as
follows:

> -   DeletionQV
> -   InsertionQV
> -   MergeQV
> -   SubstitutionQV
> -   DeletionTag

To find out if your cmp.h5 file is loaded with these QV tracks, run the
command :

    % h5ls -rv aligned_reads.cmp.h5

and look for the QV track names in the output. If your cmp.h5 file is
lacking some of these tracks, Quiver will still run, though it will
issue a warning that its performance will be suboptimal.

Why is quiver/arrow making errors in some region?
=================================================

The most likely cause for *true* errors made by these tools is that the
coverage in the region was low. If there is 5x coverage over a 1000-base
region, then 10 errors in that region can be expected.

It is important to understand that the effective coverage available to
quiver/arrow is not the full coverage apparent in plots---the tools
filter out ambiguously mapped reads by default. The remaining coverage
after filtering is called the /effective coverage/. See the next section
for discussion of MapQV.

If you have verified that there is high effective coverage in the region
in question, it is highly possible---given the high accuracy quiver and
arrow can achieve---that the apparent errors actually reflect true
sequence variants. Inspect the FASTQ output file to ensure that the
region was called at high confidence; if an erroneous sequence variant
is being called at high confidence, please report a bug to us.

What does Quiver do for genomic regions with no effective coverage?
===================================================================

For regions with no effective coverage, no variants are outputted, and
the FASTQ confidence is 0.

The output in the FASTA and FASTQ consensus sequence tracks is dependent
on the setting of the `--noEvidenceConsensusCall` flag. Assuming the
reference in the window is "ACGT", the options are:

  ---------------------------------------------------------
  `--noEvidenceConsensusCall=...`                Consensus
                                                 output
  ---------------------------------------------- ----------
  `nocall` (default in 1.4)                      NNNN

  `reference`                                    ACGT

  `lowercasereference` (new post 1.4, and the    acgt
  default)                                       
  ---------------------------------------------------------

What is MapQV and why is it important?
======================================

MapQV is a single scalar Phred-scaled QV per aligned read that reflects
the mapper's degree of certainty that the read aligned to *this* part of
the reference and not some other. Unambigously mapped reads will have a
high MapQV (typically 255), while a read that was equally likely to have
come from two parts of the reference would have a MapQV of 3.

MapQV is pretty important when you want highly accurate variant calls.
Quiver and Plurality both filter out aligned reads with a MapQV below 20
(by default), so as not to call a variant using data of uncertain
genomic origin.

This can be problematic if using quiver/arrow to get a consensus
sequence. If the genome of interest contains long (relative to the
library insert size) highly-similar repeats, the effective coverage
(after MapQV filtering) may be reduced in the repeat regions---this is
termed these MapQV dropouts. If the coverage is sufficiently reduced in
these regions, quiver/arrow will not call consensus in these
regions---see
What do quiver/arrow do for genomic regions with no effective coverage?\_.

If you want to use ambiguously mapped reads in computing a consensus for
a denovo assembly, the MapQV filter can be turned off entirely. In this
case, the consensus for each instance of a genomic repeat will be
calculated using reads that may actually be from other instances of the
repeat, so the exact trustworthiness of the consensus in that region may
be suspect. The next section describes how to disable the MapQV filter.

How can the MapQV filter be turned off and when should it be?
--------------------------------------------------------------The MapQV
filter can be disabled using the flag `--mapQvThreshold=0` (shorthand:
`-m=0`). If running a quiver/arrow job via SMRT Portal, this can be done
by unchecking the "Use only unambiguously mapped reads" option. Consider
this in de novo assembly projects, but it is not recommended for variant
calling applications.

How can variant calls made by quiver/arrow be inspected or validated?
=====================================================================

When in doubt, it is easiest to inspect the region in a tool like SMRT
View, which enables you to view the reads aligned to the region.
Deletions and substitutions should be fairly easy to spot; to view
insertions, right-click on the reference base and select "View
Insertions Before...".

What are the filtering parameters that quiver/arrow use?
========================================================

The available options limit read coverage, filters reads by MapQV, and
filters variants by quality and coverage.

-   The overall read coverage used to call consensus in every window is
    100x by default, but can be changed using `-X=value`.
-   The MapQV filter, by default, removes reads with MapQV \< 20. This
    is configured using `--mapQvThreshold=value` / `-m=value`
-   Variants are only called if the read coverage of the site exceeds
    5x, by default---this is configurable using `-x=value`. Further,
    they will not be called if the confidence (Phred-scaled) does not
    exceed 40---configurable using `-q=value`.

What happens when the sample is a mixture, or diploid?
-----------------------------------------------------At present,
quiver/arrow assume a haploid sample, and the behavior of on sample
mixtures or diploid/polyploid samples is *undefined*. The program will
not crash, but the output results are not guaranteed to accord with any
one of the haplotypes in the sample, as opposed to a potential
patchwork.

Why would I want to *iterate* the mapping+(quiver/arrow) process?
=================================================================

Some customers using quiver for polishing highly repetitive genomes have
found that if they take the consensus FASTA output of quiver, use it as
a new reference, and then perform mapping and Quiver again to get a new
consensus, they get improved results from the second round of quiver.

This can be explained by noting that the output of the first round of
quiver is more accurate than the initial draft consensus output by the
assembler, so the second round's mapping to the quiver consensus can be
more sensitive in mapping reads from repetitive regions. This can then
result in improved consensus in those repetitive regions, because the
reads have been assigned more correctly to their true genomic loci.
However there is also a possibility that the potential shifting of reads
around from one rounds' mapping to the next might alter borderline (low
confidence) consensus calls even away from repetitive regions.

We recommend the (mapping+quiver) iteration for customers polishing
repetitive genomes, and it could also prove useful for resequencing
applications. However we caution that this is very much an *exploratory*
procedure and we make no guarantees about its performance. In
particular, borderline consensus calls can change when the procedure is
iterated, and the procedure is *not* guaranteed to be convergent.

Is iterating the (mapping+quiver/arrow) process a convergent procedure?
=======================================================================

We have seen many examples where (mapping+quiver), repeated many times,
is evidently *not* a convergent procedure. For example, a variant call
may be present in iteration n, absent in n+1, and then present again in
n+2. It is possible for subtle changes in mapping to change the set of
reads examined upon inspecting a genomic window, and therefore result in
a different consensus sequence there. We expect this to be the case
primarily for "borderline" (low confidence) base calls.

SEE ALSO
========

**variantCaller**(1)
