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?
•
written
by
kimkes25 •
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
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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