I am getting an error while running the liftOver tool http://genome.sph.umich.edu/wiki/LiftOver locally on my Mac OSX
The code I execute is as follows:
~/Downloads/liftOver ./ICBP-summary-Nature.bed ~/Downloads/hg18ToHg19.over.chain.gz ./converted_icbp_coordinates.bed ./unlifted_icbp_coordinates.bed
The error reads as following:
Reading liftover chains Mapping coordinates Expecting integer field 2 line 2146483 of ./ICBP-summary-Nature.bed, got 6.5e+07
So i checked the data on this particular line and the data seems to be fine as follows by running sed as
sed -n '2146843p' ICBP-summary-Nature.bed
and I get the following output for the line
chr16 65819026 65819027 rs3852699
The consequence of this error is that the program breaks at this line number so my remaining snps (~300,000) in the subsequent lines do not get converted.
I thought I should post this query on the UCSC Genome Support Forum here http://redmine.soe.ucsc.edu/forum/index.php, but the registration seems to have closed?
Thank you for going through my query and I would be grateful for any tips or suggestions on how to resolve this?
At the request of komal, I am posting a few lines which appear before and after this line. So the following are some of the lines before 2146843(including 2146843) are:
chr16 65787923 65787924 rs3730406 chr16 65790185 65790186 rs11700 chr16 65791635 65791636 rs8058861 chr16 65791780 65791781 rs8059662 chr16 65794844 65794845 rs13336793 chr16 65798783 65798784 rs12051247 chr16 65798928 65798929 rs12051249 chr16 65802113 65802114 rs16957240 chr16 65811920 65811921 rs7193713 chr16 65817068 65817069 rs7196793 chr16 65817164 65817165 rs7196989 chr16 65819026 65819027 rs3852699
And the following are some of the lines afterwards:
chr16 65819026 65819027 rs3852699 chr16 65819348 65819349 rs6499116 chr16 65822861 65822862 rs6499118 chr16 65829359 65829360 rs3852700 chr16 65829878 65829879 rs16957265 chr16 65835167 65835168 rs6499119 chr16 65842341 65842342 rs6499121 chr16 65847342 65847343 rs9940665 chr16 65847656 65847657 rs9931407 chr16 65850656 65850657 rs8064216 chr16 65855664 65855665 rs8053031