Merge branch 'master' of https://github.com/PapenfussLab/gridss into dev

Readme.md

@@ -165,6 +165,21 @@ At present, command line valiation is performed independently of which steps are
 
 Just specify multiple BAMs on the command line. GRIDSS will perform joint calling and provide a per-BAM breakdown of support.
 
+### Should I do joint calling or run each sample individually?
+
+**Joint calling should always be used for related samples** (e.g. tumour/normal or trio calling).
+Joint calling will ensure that a common variant near the single-sample threshold of detection will be reliably reported as a shared variant.
+This is not the case if the calling were done individually.
+Note that this particular behaviour is not specific to GRIDSS and is common to all variant callers (hence the joint calling support in many callers).
+
+Joint calling allows for sensivity detection of variants that are present subclonally (or at low coverage) that would not be detected if called individually.
+
+GRIDSS performs joint assembly then reports a per-sample breakdown. Joint calling has higher coverage of shared variants thus resulting in more reliable assembly of that variant.
+
+Determining whether two SV calls in two different VCFs are actually the same call is non-trivial.
+Imprecise calls are especially problematic since the coordinates may differ between the VCF, or a call may be precise in one VCF and not in the other.
+A good example of why reconciling SV calls is so problematic is the case where call A (chrX:1-99->chrY:1-99) overlaps call B (chrX:50-149->chrY:1-99), call B overlaps call C (chrX:100-199->chrY:1-99), but A does not overlap C at all. Joint calling obviates this step.
+
 ### How do I perform tumour/normal somatic variant calling?
 
 Jointly call on all samples from the patient.

VIRUSBreakend_Readme.md

@@ -109,6 +109,7 @@ Each viral integration should have 2 integration breakpoints (one for the start,
 The key differentiator of VIRUSBreakend is the ability to detect and classify integration sites in repetative sequences such as centromeres.
 Due to the repetative nature of these region, such integration sites cannot be unambigously placed in the host genome.
 In such cases, the mapq encoded in the `BEALN` field will be 0 and the field may contain multiple candidicate integration sites.
+Integration sites in which the reported position is ambiguous have a `LOW_MAPQ` FILTER applied.
 
 The `INSRM` field contains the repeat sequences identifed in the integration site host sequences.
 These annotations can be used to classify ambigous integration sites.