bed file indexing problem
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Entering edit mode
11 months ago
kimkes25 ▴ 30

Hello.

I have a bed file that looks like this:

Capture4

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 problom after trying the second action, it returns this error :"Unsorted positions on sequence #1: 244318174 followed by 1179391"

what can I do?

samtools tabix bed bed file dnase1 • 1.2k views
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1
Entering edit mode
11 months ago
ATpoint 54k

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.

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0
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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
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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.

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