tabix

What extension should the tab-delimited pileup have?

Answer: 

For general instructions on preparing the pileup format
http://genomeview.org/content/preparing-pileup

For the tab delimited file, you should include .swig somewhere in the filename.

We typically end up with something like:
bigfile.bam.swig.bgz

Feature indexing fails - Tabix segmentation fault

Answer: 

We have identified issues that can result in tabix giving a segmentation fault.

1) Tabix does not support the UCSC header line. You'll have to remove this line
track name=blabalh description="more blah blah"

2) Columns in a bed/gff file must be seperated with tab characters, not with regular spaces. Tabix will give a segmentation fault when trying to index a file with spaces instead of tabs.

3) There should be no comment lines (lines starting with #) in the bed/gff file.

4) There should be no empty lines, or lines with only white spaces.

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