LiftOver h19 to canFam3

[Cooks]

Hi all,

I am trying to convert hg19 coordinates to canFam3 coordinates ( in *.bed format obviously) but liftOver does not seem to work when I run it on my local workstation and I am at a loss here since it does not give me any error message other then displaying the standard - no argument lines, telling me what options I can use.

If I use the webinterface, everything works fine but since I am doing some comparative genomics I have the issue of having 50+ bed files some of them rather large which I can not submit to the webtool ( and I am not a mad man ).

I tested the liftOver webapp with some of the smaller files and, as I mentioned, it worked fine but the command line tool just will not work.

I have the appropriate chain file:

hg19ToCanFam3.over.chain

and here is my smallest input file for the liftOver (Assume its name is Test.bed):

chr1	234729019	234729149
chr10	5004629	5004761
chr10	5046900	5047032
chr10	5090053	5090163
chr10	5135601	5135732
chr10	5178406	5178457
chr10	5178714	5178738
chr10	5237873	5237937
chr11	123172099	123172232
chr12	74158057	74158194

Testing with this file and others the webinterface produces a good output.

Here are the commands I tried on the command line:

liftOver Test.bed hg19ToCanFam3.over.chain -minMatch=0.1

liftOver Test.bed hg19ToCanFam3.over.chain -minMatch=0.1 > newFile

liftOver -minMatch=0.1 -tab Test.bed hg19ToCanFam3.over.chain newFile

... and many more - since there is very little documentation ( at least I found none) on how to use this tool, I am at a loss.

I hope somebody has an idea or notices something very obvious that I am doing wrong here.

Thanks in advance for your help!