VCF

Owned by Cyrielle Kint
Last updated: May 02, 2022
3 min read

New sample - Import SNV VCF

A new sample is created in Moon upon uploading a VCF file containing the single nucleotide variants and small indels (SNVs) called based on NGS data. This NGS data can result from sequencing targeted gene panels, whole exomes or whole genomes.

The following needs to be taken into account with regard to the input VCF files:

Divergence of the file format from the VCF specifications can interfere with correctly reading, annotating and analysing the files and hence can impact the output of the analysis.

  • Moon supports VCF files called against both genome builds GRCh37 and GRCh38. Based on information in the VCF header, the software extracts the genome build, and annotates the file accordingly during analysis. More specifically, if a ‘Reference’ field is present in the header, the info provided in this field is used to determine the genome build (either hg19/GRCh37 or hg38/GRCh38). If no specific ‘Reference’ field is available in the VCF header, the software checks for the presence of ‘hg38’ or ‘GRCh38’ in the entire header. If this is present, GRCh38 is assigned. In case the VCF header contains no indication of the genome build or only contains ‘hg19’ or ‘GRCh37’, genome build GRCh37 is assigned.
    The genome build used for annotation of the file is displayed on the Quality page of the sample.

  • For mitochondrial DNA, the Revised Cambridge Reference Sequence (NC_012920.1) should be used as reference.

Mitochondrial variants called against another reference will be incorrectly annotated, which will cause incorrect results.

  • Each sample should be uploaded as a separate VCF file.

Multiplex VCF files are not supported by Moon. Performing an analysis on a Multiplex VCF file can lead to incorrect results.

  • Although Moon supports import of gVCF files, 0/0 calls are not taken into account for annotation and analysis.

  • Haplotypes/patch chromosomes are not annotated or considered during analysis.

 

The steps below indicate how to manually upload a VCF file with SNV calls:

  • Go to the Samples screen (menu at the top left of the screen).

  • Click the New Sample button at the top right of the screen

  • Drag and drop one or more (gzipped) VCF files in the upload area.

  • Once a file is uploaded, the sample appears on top of the Sample list. By default, Moon displays the VCF file name as sample name.

Moon also provides an API to automatically import VCF files from an existing pipeline.

Import SV/CNVs

A file containing structural variant calls (SV) and copy number variation (CNV) can be optionally added to an existing sample on the Patient Info screen. These variants can be provided either in VCF format (according to the specifications defined at https://samtools.github.io/hts-specs/VCFv4.3.pdf) or as output from Nexus Copy number.

The following fields are required in SV/CNV VCF files in order to allow a Moon analysis:

  • Chromosome

  • Position

  • END (defined in INFO field)

  • SVTYPE (defined in INFO field)

  • GT (genotype)

If copy number is provided in the VCF (CN), this info will be taken into account. If this is not available, CN will be annotated based on the genotype information.

 

For Nexus Copy number files, the following information should be included in the uploaded file:

  • Chromosome Region (genomic coordinates of the event)

  • Event (CN Gain / CN Loss / Homozygous Copy Loss)

 

To add an SV file to an existing sample, either a proband or a healthy family member, follow the steps below:

  • On the Samples screen, click the Patient info icon next to the sample name of interest.

  • Drag and drop the file corresponding to the sample of interest in the upload area at the bottom of the screen.

  • Once the SV file is uploaded. Moon displays the SV VCF file name. You have the option to remove the SV file by clicking Remove it.