Description of inputs

aSCNA segmentation file:

Tab delimited allelic copy number segmentation file:

Chromosome	Start	End	f	tau
1	12191	6524781	0.5	2.20
1	6579504	53323421	0.196	3.08

Required fields:

Start: Genome basepair of start of copy number segment.

End: Genome basepair of end of copy number segment.

Chromosome: Chromosome of copy number segment.

f: Mean allele fraction of minor parental allele at this segment. This corresponds to the allele imbalance observed in inherited (germline) SNPs at this locus. For example a one copy amplification would yield a 2:1 ratio of parental alleles the germline variants within a segment of this locus would be centered around 0.66 and 0.33 allele fractions. As a matter of convention f represents the minor fraction (0.33).

tau: Two centered segment copy ratio data. Copy ratio is the relative amount of DNA in the tumor sample at the segment compared to normal (or a panel of normals). We use this ratio plus 2.

SNP statistics file:

Tab delimited file with reporting the allele counts for inherited variants. DeTiN expects two of these files one with read counts from the normal sample and the other from the tumor sample:

Chromosome	position	ref_count	alt_count
1	762273	164	41
1	808631	23	17

Required fields:

Chromosome: chromosome of germline variant.

position: genomic position of germline variant.

ref_count: reference allele count for germline variant.

alt_count: alternate allele count for germline variant.

Mutation statistics file:

Note that if using Strelka use version v.2.9.7. This version has fixed some of the hard filtering which is problematic in earlier versions. Thanks to MagdalenaZZ for pointing this out.

Tab delimited file with reporting the allele counts and quality of candidate somatic variants.

Chromosome	position	n_alt_count	n_ref_count	t_alt_count	t_ref_count	failure_reasons	judgement
1	762273	3	50	45	61	alt_allele_in_normal	REJECT
1	808631	0	17	30	80		KEEP

Required fields:

contig: chromosome of candidate variant.

position: genomic position of candidate variant.

n_alt_count: alternate allele count in the normal sample.

n_ref_count: reference allele count in the normal sample.

t_alt_count: alternate allele count in the tumor sample.

t_ref_count: reference allele count in the tumor sample.

failure_reasons: reason for rejecting the variant (blank for kept sites). Sites which are just rejected for evidence in the normal should be rejected with the failure reason 'alt_allele_in_normal'.

judgement: REJECT for rejected sites and KEEP for kept sites.