tabix a text file

Question

[vigprasud]

Is there a way to tabix a text file and use it for quick retrieval of records?

I have these fields in a text file

#CHR START STOP GENE

I would like to retrieve the records based on chr:start-pos.

My sample file [sample.txt] has this data

chr1    11873   14361   A
chr1    14469   29370   B
chr1    34610   36081   C
chr1    69090   70008   D
chr1    134772  140566  E
chr1    323891  328581  F
chr1    367658  368597  G

I bgzipped it to get sample.txt.gz file

I tabixed with the following command

tabix -b 1 -e 3 -S 0 -0 sample.txt.gz

and this is the error I encountered

[get_intv] the following line cannot be parsed and skipped: chr1        11873   14361   A
[ti_index_core] the indexes overlap or are out of bounds

Any ideas on how to tabix a text file?

Answer 1

[Pierre Lindenbaum]

'start' is in column 2 , you used -b 1

You'd better use the predefined setting tabix -p bed