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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Type of PE in the FORMAT from vcf is set as integer - should be float #269

Open miyakokodama opened 2 years ago

miyakokodama commented 2 years ago

Hi,

I have CNVpytor on a GIAB sample, and have used cnvnator2VCF.pl (CNVnator v.0.4.1) to convert the tsv file to .vcf.

Of the 3 fields below in FORMAT of the vcf file, I have noticed that the type for PE is set as integer:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-ends that support the event">

However, this field has digits so it should be coded as float in the header (GT:CN:PE).

1/1:0:0.9980
1/1:0:0.0000
0/1:1:0.0329

Could you please make this change in the script?

Thanks, Miyako