SNV VCF

Owned by Sara Haers
Apr 29, 2022
2 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:

  • Recommended: compress the VCF files of interest as a gzip file (see Gzip for more information)

  • 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.