representation of chromosomal positions in the format of cytogenetic band.

Question

[sktbanerjee1]

Hello, I have some variants in standard vcf format. I want to represent them in [chromosome no][arm name] [band position] based location. is there any way i can convert my positions in this format using some tool. Thanks in advance.

Answer 1

[Pierre Lindenbaum]

use bedtools intersect with your vcf and the UCSC cytoband as a BED file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz