liftOver command line tool

[Onur Sumer]

Hello,

I am using the command line liftOver tool (for 64-bit linux) together
with the chain file hg18ToHg19.over.chain to convert genome coordinates
from hg18 to hg19. Command line tool fails to convert most of the single
position coordinates, in other words coordinates with the same start and
end positions cannot be converted.

Below is an example line from the input file:

chr17 7520197 7520197

And the output in the unmapped file for these coordinates is:

#Deleted in new
chr17 7520197 7520197

However, when I use the web-based version
(http://genome.ucsc.edu/cgi-bin/hgLiftOver), the same data is
successfully converted from hg18 to hg19.

Here is the input that works for the web-based version:

chr17:7520197-7520197

And the conversion result is:

chr17:7579472-7579472


Do you have an idea why the command line tools does not work for such
coordinates. Are the default parameters of the web-based version
different than the command-line version? Or, can it be a bug in the
command line tool? Or, maybe I am missing some point.

Thanks,
Onur Sumer
Computational Biology Center,
Memorial Sloan Kettering Cancer Center

[Brooke Rhead]

Hi Onur,

BED coordinates are zero-based, half-open. See:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1
and
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms

The coordinate range "chr17 7520197 7520197" in BED format specifies a
region of size 0. Instead, use:

chr17 7520196 7520197

(This is equivalent to chr17:7520197-7520197, which is what we call
"position" format . . . this is the same format you see in the Genome
Browser.)

When I convert the corrected BED coordinates using the web interface, I get:

chr17 7579471 7579472

(which is equivalent to chr17:7579472-7579472 in position format).

If you have further questions, please contact us again at
***@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

Post by Onur Sumer
Hello,
I am using the command line liftOver tool (for 64-bit linux) together
with the chain file hg18ToHg19.over.chain to convert genome coordinates
from hg18 to hg19. Command line tool fails to convert most of the single
position coordinates, in other words coordinates with the same start and
end positions cannot be converted.
chr17 7520197 7520197
#Deleted in new
chr17 7520197 7520197
However, when I use the web-based version
(http://genome.ucsc.edu/cgi-bin/hgLiftOver), the same data is
successfully converted from hg18 to hg19.
chr17:7520197-7520197
chr17:7579472-7579472
Do you have an idea why the command line tools does not work for such
coordinates. Are the default parameters of the web-based version
different than the command-line version? Or, can it be a bug in the
command line tool? Or, maybe I am missing some point.
Thanks,
Onur Sumer
Computational Biology Center,
Memorial Sloan Kettering Cancer Center
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