vcf2cytosure

This tool converts a VCF with structural variations to the “.CGH” format used by the commercial CytoSure Interpret Software by OGT (Oxford Gene Technology). CytoSure is made for displaying oligo array measurements. It works on a set of probes, which this tool emulates.

Usage

Cytosure requires an input vcf file. Optionally, a coverage bed or snp vcf file could be used to visualise the coverage across the genome.

INSTALL:
    git  clone https://github.com/NBISweden/vcf2cytosure.git
    cd vcf2cytosure
    pip install -e .

or use Singularity  

    singularity pull shub://J35P312/vcf2cytosure

RUNNING:
    
vcf2cytosure --vcf <input.vcf> --out <output.cgh>

optionally

vcf2cytosure --vcf <input.vcf> --out <output.cgh> --coverge <overage.bed> --sex <male|female>

or:

vcf2cytosure --vcf <input.vcf> --out <output.cgh> --snv <snv.vcf> --sex <male|female>

The coverage bed file may be created using TIDDIT(https://github.com/J35P312/TIDDIT)

TIDDIT --cov -b <input.bam> -o <coverage_pefix>

The binning of the input coverage file may be controlled using the –bins parameter:

vcf2cytosure --vcf <input.vcf> --out <output.cgh> --snv <snv.vcf> --bins 50

Here 50 coverage bins will be pooled into one probe. The number of probes affect the amount of detail and resolution in the analysis. A large number of probes will make cytosure sluggish.

Structural variants

Structural variant (SV) types DEL, DUP, TDUP, IDUP, INV, and INS are supported. For each SVs, at least three probes are generated. If the SV is large enough, then more probes are generated that are spaced 100 kbp apart.

The SVs are displayed in the following way.

• DEL (Deletions): Probes at height -1
• DUP (Duplication): Probes at height +1
• TDUP (Tandem duplication): Probes at height +1.5

For each SV, an aberration record is also generated. The attributes are filled in the following way:

• “Confirmation Method” is set to the type of the SV (DEL, INS, DUP, etc.)
• “# Probes” is set to the OCC value found in the input INFO field (number of occurrences in the reference population)
• The “Comment” field contains all the INFO attributes that have not otherwise been used for one of the above fields.
• The copyNumber field is set to the RankScore value from the VCF INFO field
• The other attributes are set to some arbitrary, but constant value.

If the --coverage option is used, probe heights will represent coverage. Coverage is represented as log2 ratios of input bin coverage relative to all bin coverages, limited at [MIN_HEIGHT, MAX_HEIGHT]. This means probes are drawn at height 0 if the coverage corresponds to the average coverage, at 0.58 for a heterozygote duplication, 1 for double average coverage, -1 for a heterozygous deletion and at around -MAX_HEIGHT for little or no coverage.

High or low average coverages are clamped to a height of +/-4 and are not shown at their actual height.

If the --coverage option is not used, evenly spaced probes with height 0.01 (height 0.0 would not be shown by CytoSure) are generated for the areas between SVs.

Notes on the file format

• CGH is in XML format. The company does not seem to have a schema file.

• The parser in CytoSure accepts reformatted XML files. This is ok:

  xmllint --format file.cgh > pretty.xml

• One probe can be made up of more than one spot:

  <probe ...>
    <spot ... />
    <spot ... />
  </probe>

• The probes in the file do not have to be sorted by chromosome and/or coordinate.

• There are <probe> elements without sequence, without chromosome name:

  <probe name="probename" sequence="">
    <spot index="56774" row="334" column="164" red="123.4" green="345.6" gSNR="1.0" rSNR="50.0" outlier="false"/>
  </probe>

• Coordinates are 1-based (since stop - start = 59 and length of sequence is 60)

• Removing the ‘sequence’ attribute does not work, but setting it to a fake one does

• The log2 ratio is computed as log2(green/red)

• Normalization segments look like this:

  <segment chrId="1" numProbes="10" start="7000" stop="1000000" average="-0.003"/>

• Segments can overlap each other

• Names “X” and “Y” are not used for the corresponding chromosomes. Instead, the X chromosome is stored as 23, they Y chromosome as 24 (in probes, segments and aberrations).

• N_INTERVALS for hg38 were taken from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/gap.txt.gz.