VCF files missing some chromosomes info
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9 weeks ago

My vcf files show chromosome variants till chromosome 14, though in upper info for contigs it mentions lengths from chr 1 to 22 and X and Y. Is that normal that vcf files get missed on some info?

chromosome VCF infos Missing • 203 views
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Entering edit mode
9 weeks ago

It sounds like your question is whether the file has been filtered or not.

When a VCF file is created the tool does not know "beforehand" which segments will have variants, hence will produce headers for all the segments in the BAM file.

The VCF header is generated before any other variant is produced, thus it will contain all information.

But then, of course, in a realistic scenario, it would be impossible that there would be no variants in the other chromosomes unless there was no coverage in the original data.

Thus the data is filtered in some way, perhaps after the VCF was created, but perhaps before that, by only covering certain regions.

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