Reference Transcript Mismatch Reporter

This tool can be used to identify variants where the reference genome build doesn’t match the Ensembl reference transcript used by VEP for variant consequence annotations. In these cases, the REF nucleotide(s) at a variant position will differ from the Ensembl transcript nucleotide(s) at the corresponding mutation position. Any resulting amino acid change predictions found in the Amino_acids field of the VEP CSQ annotation will then be different from the translated Ensembl transcript amino acids at that position.

This will lead to errors in some downstream tools, e.g. pVACseq, which rely on the Amino_acids field as well as the translated Ensembl transcript peptide sequence - as reported by the Wildtype plugin to make predictions about the impact of the mutation on the transcript peptide sequence. Since those two fields will be in disagreement in such cases as described above, pVACseq cannot make predictions on such variants.

Such errors might occur in a small number of variants if there are only minor differences between the reference used and the Ensembl transcripts but they might also be more widespread, for example, if users aligned to GRCh37 but used a GRCh38 VEP cachce.

The input VCF needs to be annotated by VEP and requires annotation with the Wildtype VEP plugin available as part of pVACtools.

This tool will report on the number of variants and transcripts in a VCF that are affected by this issuei and output this information to stdout. It will write a .mismatch.tsv file next to the VCF that provides further details on the problematic variants.

This tool also allows the user to either soft-filter or hard-filter the VCF using the --filter [soft|hard] parameter. Soft-filtering will tag the problematic variants with a custom VCF FILTER CSQ_MISMACH while hard-filtering will produce a new VCF that has these variants removed. When using a filter, the output VCF will be written to a filtered.vcf file next to your input VCF file. You can set a different output file using the --output-vcf parameter.


usage: ref-transcript-mismatch-reporter [-h] [-f {soft,hard}] [-o OUTPUT_VCF]

A tool to identify variants in a VCF where the reference genome used to align
and call variants doesn't match the Ensembl reference transcript used by VEP
for variant consequence annotations.

positional arguments:
  input_vcf             A VEP-annotated VCF file with Wildtype plugin

optional arguments:
  -h, --help            show this help message and exit
  -f {soft,hard}, --filter {soft,hard}
                        soft: Write a soft-filtered VCF file which identifies
                        variants with mismatched VEP annotations with the
                        CSQ_MISMATCH filter. hard: Write a hard-filtered VCF
                        file that removes variants with mismatched VEP
  -o OUTPUT_VCF, --output-vcf OUTPUT_VCF
                        Path to write the output VCF file to if a --filter is
                        chosen. If not provided, the output VCF file will be
                        written next to the input VCF file with a
                        .filtered.vcf file ending.

Example Command

csq-mismatch-report input.vcf --filter soft