Small Mutations

Small mutations are composed of indels and single nucleotide variants. These should be passed to the IPR python adapter in the main report content JSON.

{
    "smallMutations": [
        // variants
    ]

}

Each variant is an object which may contain any of the following fields

Field	Type	Example	Description
altSeq (required)	string	"C"	the alternate sequence
chromosome (required)	string	"X"	the chromosome this mutation is located on
endPosition (required)	integer?	1234	the genomic end poition of this variant
gene (required)	string	"KRAS"	the gene name
proteinChange (required)	string?	"p.G12D"	the HGVS protein notation. Can also be the cds or genomic notation for variants where there is no equivalent protein notation. Protein notation is preferred.
refSeq (required)	string?	"A"	the reference sequence
startPosition (required)	integer?	1234	the genomic start position of this variant
transcript (required)	string?	"ENST00001.2"	the transcript name
detectedIn	string	"DNA/RNA"	the sample types this variant was detected in
hgvsCds	string?	"ENST0001:c.1234+3A>G"	HGVS coding sequence notation for this variant
hgvsGenomic	string?	"1:g.1234A>G"	HGVS genomic notation for this variant
hgvsProtein	string?	"KRAS:p.G12D"	HGVS protein notation for this variant
ncbiBuild	string?	"GRCh37"	the genome reference assembly build version
normalAltCount	integer?	1	the number of alternate reads in the normal genome supporting the mutation
normalDepth	integer?	1	the total number of reads at this position in the normal genome
normalRefCount	integer?	1	the number of reference reads in the normal genome
rnaAltCount	integer?	1	the number of alternate reads in the rna supporting the mutation
rnaDepth	integer?	2	the total number of reads at this position in the rna
rnaRefCount	integer?	1	the number of reference reads in the rna
tumourAltCount	integer?	1	the number of alternate reads in the tumour genome supporting the mutation
tumourDepth	integer?	2	the total number of reads at this position in the tumour genome, if not given this will be inferred based on the ref and alt count sum
tumourRefCount	integer?	1	the number of reference reads in the tumour genome
zygosity	string?	"het"