Question: Sorting with vcftools for tabix gone wrong
1
gravatar for axelwilhelm
4.6 years ago by
axelwilhelm100
Sweden
axelwilhelm100 wrote:

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?

index vcftools sort tabix vcf • 4.0k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 4.6 years ago by axelwilhelm100
2
gravatar for Istvan Albert
4.6 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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?

ADD COMMENTlink written 4.6 years ago by Istvan Albert ♦♦ 80k

No, should I?

ADD REPLYlink written 4.6 years ago by axelwilhelm100
1

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

ADD REPLYlink written 4.6 years ago by axelwilhelm100
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