I have to say that the VCF file is all tab separated. So, there are the first 20 lines of my vcf file:
t1 > > > > then bgzip and tabix, I got this error. > > ~/bin/tabix -s 1 -b 2 -e 3 genePosition.gz > > [ti_index_core] the file out of order at line 88 > ...
[ti_index_core] the file out of order at line 176099 Error in value[[3L]](cond) : internal: samtools invoked 'exit(1)'; see warnings() and restart R file: ...
line 23, in run _do_run(cmd, checks, log_stdout) File
Only GVCF files produced by HaplotypeCaller (or CombineGVCFs) can
pairix -s 1 -d 4 -b 2 -e 3 -u 5 -v 6 -T 3R.txt.gz. but I get. [get_intv] the following line cannot be parsed and skipped: chr3R 0 20000 chr3R 40000 60000 252. [ti_index_core] the indexes overlap or are out of bounds.
With multiple files works as a switch on the command line, see the example
[ti_index_core] the indexes overlap or are out of bounds
NAME. tabix – Generic indexer for TAB-delimited genome position files
I am trying to use vcf-merge on 2 of my vcf files in order to carry out an Fst analysis in the software; for that I need to use tabix and vcf-sort to ...