Alan -
Yes, tabix works fine for indexing and retrieval from
multi-chromosome files. It relies on the extra fields
provided by bgzip compression, not simply gzip. I think
it doesn't work on uncompressed files. The entries for
each chromosome must be sorted. Chromosome in column 1
and position in column 2 should be close enough to .vcf
format so that tabix will work with no additional
arguments. Give it a try.
- tom blackwell -
On Sun, 3 Sep 2017, Alan Achenbach wrote:
Can tabix be used to index multi-chromosome files? What is used for begin and
end if I have chromosome in column one and position in column two of a non-vcf
file?
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