new regions in GRCh38

Question

[skanterakis]

Hello, I wanted to inspect the (non-N) regions that were added in, in GRCh38/hg38 that were not there in GRCh37/hg19. Is there a hg38 bed file with those "new" regions somewhere or is there an easy way to get that without lifting over again? Thanks for your help!

[natasha.sernova]

See these posts:

A: How to determine reference genome that was used for alignment given BAM with obs

A: Convert BED(UCSC) to VCF

Answer 1

[skanterakis]

I used the excellent remap service from NCBI: http://www.ncbi.nlm.nih.gov/genome/tools/remap

to go from my hg19 assembly to my hg38 assembly.

I made a dummy bed file using the chromosome lengths, which you can get from here:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom, size from hg19.chromInfo" > hg19.genome

and selected:

Minimum ratio of bases that must be remapped: 0

Maximum ratio for difference between source length and target length: 100000

and that gave me all possible mappings.