The BAM file is sorted using: samtools sort KAPA.bam KAPA.sorted The BED file is sorted using: sort -k1,1 -k2,2 regions.bed > regions.sorted.bed I invoke the bedtool.
bioinformatics.stackexchange.com
out ERROR: chromomsome sort ordering for file input.bam is inconsistent with other files. Tracking this down I find that samtools sort , which was executed on the .
By default, bedtools sort sorts a BED file by chromosome and then by start position in ascending order. For example: cat A.bed chr1 800 1000 ...
I also tried sorting the alignment-derived bed-file in the same way, as I did with ...
When using the -sorted option with files whose chromosomes are not
For both closest and fisher, bedtools is returning errors for genome file having no valid entries
The merge tool requires that the input file is sorted by chromosome, then by start ... one can also merge intervals that do not overlap, yet are close to one another.
We use chromosome conformation capture mapping to derive the linear order of ... only the smallest elements, namely Mariners, to be tolerated closest to genes. ... Duplicate removal and sorting were performed with NovoSort
genomebiology.biomedcentral.com
However, comprehensive variant annotation with diverse file formats is
HelloRanges provides an R function corresponding to each bedtools