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
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?