VCF file
The CPSR workflow accepts a single input file, which is an unannotated, single-sample VCF file (>= v4.2) with germline calls (SNVs/InDels)
- We strongly recommend that the input VCF is compressed and indexed using bgzip and tabix
- If the input VCF contains multi-allelic sites, these will be subject to decomposition. Either way, we encourage that users prepare the input VCF without the presence of multi-allelic sites.
- Variants used for reporting should be designated as ‘PASS’ in the VCF FILTER column
- In order for CPSR to report the genotypes of individual variants in cancer predisposition genes (hom/het), the VCF file needs to contain the sample-specific genotype data (i.e. a FORMAT field + sample-specific genotype field pr. VCF record)
- If the sample-specific FORMAT field contains a read depth annotation
(
DP), CPSR will capture this as the sequencing depth of each variant. Variants with a low depth (< 10X) are automatically flagged with a visual marker in the variant classification tables of the report, since a low-confidence genotype call also undermines the reliability of the variant’s clinical classification. This flag is a safety net, not a substitute for good input data - we still strongly encourage users to ensure sufficient depth of coverage among the variants submitted for CPSR analysis
IMPORTANT NOTE : CPSR generates a number of VCF INFO annotation tags that is appended to the query VCF. We will therefore encourage the users to submit query VCF files that have not been subject to annotations by other means, but rather a VCF file that comes directly from variant calling. If not, there are likely to be INFO tags in the query VCF file that coincide with those produced by CPSR.