matching relationship between the old and new coordinate lists after liftover

Question

[Dejian]

I have two genotype tables, one for parents generated from snp arrays following hg18 coordinates, and the other for their offspring generated from ngs following hg19 coordinates. I finished liftover from hg18 to hg19 for parental data (refer to this post) and I got a new list of coordinates, but I found I couldn't merge the parental genotype with the new hg19 coordinates because I don't know how to pair the new coordinates with the old ones. I wonder if there is a way to get their matching relationship. Any idea? Thanks.

[Ashutosh Pandey]

I use BED format and have some identifiers in the fourth column and they are also present in the output file after the lift over and can be used to relate genomic positions.

[Dejian]

Did you use ref snp ids (rs#)? I included ref snp id in the 4th column and they were in the liftover output. But these ids should also be lifted over to a newer version (refer to Genome Coordinates Between Assemblies: Liftover A Snp Array). In addition, some of these ids map to multiple genomic loci, making them not suitable for matching the two lists.

[parveenkayenat]

Hi,

I perform the liftover and get the results of changed coordinate but i am not sure whether i got the correct results. Below is the glimpse of submited file and the result file. I put the parameters, Source assembly = GRCh37.p13 :: Primary Assembly and Target assembly = GRCh38.p11 :: Primary AssemblyAdditionally, does the allele information are same in build37 and build38?

Input File :

1:752566
1:752721
1:752894
1:753474
1:754503
1:754964
1:758144
1:759700

Output File from NCBI remapping :

Feature SRC intervals Remap intervals Src location Src length Map location Map length Covering
Line:1  1   1   1:752566    1   1:817186    1   1.00000
Line:2  1   1   1:752721    1   1:817341    1   1.00000
Line:3  1   1   1:752894    1   1:817514    1   1.00000
Line:4  1   1   1:753474    1   1:818094    1   1.00000
Line:5  1   1   1:754503    1   1:819123    1   1.00000
Line:6  1   1   1:754964    1   1:819584    1   1.00000
Line:7  1   1   1:758144    1   1:822764    1   1.00000
Line:8  1   1   1:759700    1   1:824320    1   1.00000

Please help me in this regard, whether i got the correct results or not?

Thanks in advance

[Ram]

Do not add answers unless you're answering the top level post. Use comments or comment-replies as appropriate instead. I've moved your post to a comment now, but please be more careful in the future.

[ATpoint]

Please open a new question and add the code you used. it is unlikely you get help in such an old thread.

Answer 1

[Dejian]

Thanks, Ashutosh. Problem solved. I changed the 4th column to unique IDs, eg 1.rs#, 2.rs#, 3.rs#. Then my worries are gone.