liftover using genome browser

liftover using genome browser

0

Hello everyone,

I have a file which is hg38 build. I want to do a liftover and change it to hg19. I thought of using liftover tool from UCSC genome browser. I realise that the input file should be bed format.

My file has only two part: chrom and position. This is how my file look:

CHROM_POS
chr10_100009635
chr10_100187980
chr10_100229692
chr10_100267650

Or more detail file is:

GENE RSID1 RSID2 VALUE
ENSG00000000457.13 chr1_169894240_G_T_b38 chr1_169894240_G_T_b38 0.1736259917762202
ENSG00000000457.13 chr1_169894240_G_T_b38 chr1_169891332_G_A_b38 0.09154263431207886
ENSG00000000457.13 chr1_169891332_G_A_b38 chr1_169891332_G_A_b38 0.5075352470673014

Can anyone please tell me how should I convert this format to bed format or maybe I can use some other tool for liftover.


vcf


liftover


bed

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