LiftOver for single positions

[Buzz0r]

Hey,

does anyone know a tool to liftover form hg18 to hg19 for a file of the format:

#CHROM POS ID REF ALT QUAL FILTER INFO
1 533 . G C -1.0 0 AA=.;AC=6;AN=120;DP=423
...

problem is that it only holds the start position and not a range as liftover would like to see.

thanks, for all help.

merry xmas and a happy new year folks!

tom

[johnny]

you can just duplicate your positon and make a file like:

chr1:533-533

for input in:

http://genome.ucsc.edu/cgi-bin/hgLiftOver

this will do the trick.

my suggestion is to make this in excel, then you can just paste the converted coordinates in a new column.

[Buzz0r]

a bit tricky since my files a re too big for excel to handle...did some command line stuff with awk and made another row with it but liftOver wont take it anyways since the format is not appreaciated

got the new 1000Genomes file now and rather take that and adjust our pipeline a bit.

thanks