Expanding bed format into single nucleotide resolution

Question

[Kasthuri]

I have a TCGA CNV data:

chrom   loc.start   loc.end   num.mark   seg.mean
    1   3218610     3586250   166        0.1112

which I would like to expand as:

chrom   loc.start   seg.mean
1       3218610     0.1112
1       3218611     0.1112
1       3218612     0.1112
...
...
1       3586250     0.1112

I can easily write a code to do this, but I am afraid I will miss the actual contig numbering. Any tools out there that can do this considering the genomic coordinate information? Thanks!

Answer 1

[Alex Reynolds]

With BEDOPS bedops --chop and bedmap --echo-map-score, assuming that intervals in your cnv.txt file use a 1-based index and do not overlap:

$ tail -n+2 cnv.txt | sort-bed - | awk '{ $2-=1; print $0; }' > cnv.bed
$ bedops --chop 1 cnv.bed | bedmap --echo --echo-map-score --delim '\t' - cnv.bed | cut -f1,3,4 | cat <(echo -e 'chrom\tloc.start\tseg.mean') - > answer.txt

The file answer.txt will be formatted in a manner similar to the sample output in your question.

If your input intervals overlap or use a different index scheme, please follow up in a comment and I'll suggest a way to work with that case.

[Kasthuri]

Awesome! Thank you very much.