Does anyone know a program which can split BED file according to the chromosome? I have generate a BED file which contains the data for all chromosome, but it is not sorted. When I did sorting using BedSort, the output was not ordered according the numeric order, it always give chr10 on the top and then followed chr11, up to chr19. It seems I have to do the sorting for each chr respectively, I wonder whether there is a program which can split BED file according to the chromosome. Thanks
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You could try the following with your bed file:
Code:sort -k 1V,1 -k 2n,2 file.bed -o file.sorted.bed
Code:mkdir -p split_results for chr in `cut -f 1 file.bed | sort | uniq`; do grep -w $chr file.bed > split_results/$chr.output.bed done
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Similar to adamdeluca's suggestion, here is another simple awk solution. Note that the ">>" creates and appends to files named CHROM.bed, where CHROM is column 1 of the bed input bed file (in this case, example.bed).
So, in plain English, the awk command prints each entire line ($0) from example.bed to distinct files that are each named by the chrom field ($1).
This strategy is useful in many other cases where you want to do a context-based "grep", and route the results to distinct files.
Code:$ awk '{print $0 >> $1".bed"}' example.bed $ ls -1 *.bed chr1.bed chr2.bed ... (snip) chrY.bed example.bed
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