Sorting with vcftools for tabix gone wrong

Question

[axelwilhelm]

I concatenated two vcf files by scripting, keeping only the header from the first file and adding an extra column in the end to know which file each line is coming from.

I do this:

tabix -p vcf f1PotMut.vcf.gz

and get this:

[ti_index_core] the chromosome blocks not continuous at line 87352, is the file sorted? [pos 131430]

so I do this

vcf-sort f1PotMut.vcf.gz

but the problem remains. I get the same error when trying to tabex my "sorted" file. I somehow feel the vcf-sort command did not work. Any help?

Answer 1

[Istvan Albert]

above you are not showing but for the sake of covering that: are you redirecting the output of the vcf-sort into a different file then are you running tabix on this new file?

[axelwilhelm]

No, should I?

[axelwilhelm]

This guy does (bo-peng). Damn tools written by others.

[j.gleixner]

dead link here is archive: https://web.archive.org/web/20161104171423/http://bo-peng.blogspot.se/2011/05/upgrading-sorting-and-merging-next-gen.html