bed file indexing problem

Question

[kimkes25]

Hello

I have a bed file that looks like this:

I would like to be able to retrieve data from it using samtools with tabix.

the actions I do:

bgzip sample.bed
tabix -s 1 -b 2 -e 3 sample.bed.gz
tabix sample.bed.gz chr1:19922842-19924305

but I have a problem after trying the second action, it returns this error:

Unsorted positions on sequence #1: 244318174 followed by 1179391

what can I do?

Answer 1

[ATpoint]

A BED has no header, so get rid of it, then sort it with sort -k1,1 -k2,2n, compress with bgzip and then retry to index.

[benformatics]

Even though unix sort will probably be faster you could also sort sample.bed with bedtools (default parameters are probably fine)

bedtools sort -i sample.bed > sample_sorted.bed

[Friederike]

In addition to the first row (header), you also need to drop the first column as BED format is defined with chr, start, end in the first three columns.