How to print the header of bed file and the lines that belong to chromosome 2
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4 months ago
FadyNabil ▴ 10

I have a bed file consists of many lines and I want to extract the header and the lines that belong to chromosome 2 only in another file

fastq Bed_files fasta Bash • 282 views
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4 months ago
FadyNabil ▴ 10
awk 'NR == 1 || ($1=="chr2")' lamina.bed 
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4 months ago

If the BED file is sorted, here's a faster way:

$ cat <(head -1 regions.bed) <(bedextract chr2 regions.bed) > answer.bed

Generically, using awk to solve this will require reading through the entire file. This can be expensive for whole-genome scale files.

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