Extract chromosome arms' coordinates for specific reference

Question

I would like to get chromosome arms' coordinates for genome reference hs37d5 (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/), but I could not find them either online, or the directory listed above.

Is there a way to extract such coordinates from one of the available files (e.g., from the fasta)?

Answer 1

The chromosome sizes can be retrieved with (to use for sanity check):

> ./faSize -veryDetailed -tab hs37d5.fa.gz
1   249250621   23970000    225280621   225280621   0
2   243199373   4994855 238204518   238204518   0
3   198022430   3225295 194797135   194797135   0
4   191154276   3492600 187661676   187661676   0
...

(first column is chromosome ID, second column is chromosome size).

Afterwards, the centromere coordinates are retrieved through (in this case I used hg19 since I'm working with hs37d5):

> curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz" \
  | gunzip -c | grep acen | sed 's/chr//g' | sort -n > hg19.centromeres

The coordinates for each chromosome arm can be computed from the chromosome size and centromere coordinates.

N.B. As per UCSC documentation, cytoband's start is 0-based, while end is 1-based. As a sanity check you might want to compare the end of the last cytoband for each chromosome, with the chromosome size (they should be the same, since end is 1-based).