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tjiangHIT / cuteSV

Long read based human genomic structural variation detection with cuteSV
MIT License
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zero position in vcf #147

Closed baozg closed 2 months ago

baozg commented 2 months ago

Hi,

VCF should be 1-based coordinate system, why cuteSV report postion as 0 in the telomere region?

Meltpinkg commented 2 months ago

Hello, @baozg

According to VCF format (v4.2), the position field is indicated as: Telomeres are indicated by using positions 0 or N+1, where N is the length of the corresponding chromosome or contig. Thus the position 0 represents the SV happened in the telomere region. Hope it will help!

Best, Shuqi

baozg commented 2 months ago

Thanks. Did cuteSV will try to find TxAyGz repeat? bcftools will output warning for this location and it cannot put in a bed format, since it use 0-based format

Meltpinkg commented 2 months ago

Hello, @baozg We haven't try to find TxAyGz repeat. To use bcftools in this condition, you can make some post-processing on this vcf to avoid the warnings. I'd like to mention that the position given by cuteSV (version >= 2.0) is 1-based actually.

baozg commented 2 months ago

Thanks anyway. I will filter these variants by myself