#README.md for LiftOver Project

8/28/2019

• Using Crossmap.py via bioconda to convert bed file with 4 columns from hg19 to to hg38

• the 4th column has to be the name of the gene

• first use cut -f5-9 to get the last columns which have the new positions into an new bed file.

• these are saved in output with hg38 in name

• TODO: move 1st column to last and then write python script to attach the values from the hg19 file to the hg38 file (pandas?)

• modules needed: -- anaconda --- need to set up environment specifically for crossmap --- the chain file that is working at the moment is: GRCh37_to_GRCh38.chain