Tabix Query - End Of Chromosome.

Question

[Zev.Kronenberg]

Greetings all,

Tabix perl API documentation is sparse. I have been using it to grab chromosomes as a whole so far. Is there a way to have Tabix return the last 500kb of a chromosome without a priori knowledge of the chromosome length?

I want to avoid providing sequence length information to my script.

Answer 1

[lh3]

Unfortunately, this is not possible. BED/GFF/VCF/... does not tell tabix the chromosome lengths.

[Zev.Kronenberg]

Time for tabix 2.0 :-). The index file should contain the offset for the last SNP observed on a feature. It would also be nice if it could pull N SNPS (i.e. first 100 SNPs or last 100 SNPs ect.)