I am using a pipeline from nanopore to detect structural variants (SVs) in a human sample with long-reads sequencing. The first steps of the pipeline are:
- index the reference genome with
- map the long reads to a reference genome using same tool as above
- Get BED coordinates from the
While the first two steps uses
minimap, the third one uses a python script written by the developers of the pipeline, which can be found here.
After the pipeline calls
bamref2bed i.e. the python script above, my
target.bed looks like the following:
chr1 0 249250621 chr2 0 243199373 chr3 0 198022430 chr4 0 191154276 chr5 0 180915260 chr6 0 171115067 chr7 0 159138663 chr8 0 146364022 chr9 0 141213431 chr10 0 135534747 chr11 0 135006516 chr12 0 133851895 chr13 0 115169878 chr14 0 107349540 chr15 0 102531392 chr16 0 90354753 chr17 0 81195210 chr18 0 78077248 chr19 0 59128983 chr20 0 63025520 chr21 0 48129895 chr22 0 51304566 chrX 0 155270560 chrY 0 59373566
As far as I am concerned the first three columns of a bed file refer to (I) chr name, (II) start position (III) end position. The main thing I am wondering is how come all chromosomes have a start position of 0. Also, reading about converting bam to bed files I guess the most important feature would be the coverage across the whole chromosomes, which in this file is missing.
But my main question would be: is it normal to have a start position of 0 for all chromosomes or is there something wrong here?