Is there a NCBI eutils or something else to liftover or remap GRCh37.p13 coordinates to GRCh38 to be called from java?
1
1
Entering edit mode
7.2 years ago
burcakotlu ▴ 40

Hi to all,

As far as I know dbSNP does not allow searches for older assembly coordinates.

Therefore I need to convert GRCh37.p13 coordinates to GRCh38 coordinates before I call NCBI eutils esearch from my java code.

 

My question is as follows:

Is there a NCBI eutils or something else to liftover or remap GRCh37.p13 coordinates to GRCh38 to be called from java code?

 

Thanks in advance,

Burçak

liftover remap eutils java • 3.4k views
ADD COMMENT
0
Entering edit mode

Thank you Pierre.

Meanwhile I have used NCBI remap.

But I will try your suggestions too.

Maybe then I may have further questions.

Burçak

ADD REPLY
3
Entering edit mode
7.1 years ago

The htsjdk contains a java port of UCSC/ LiftOver : http://picard.sourceforge.net/javadoc/htsjdk/htsjdk/samtools/liftover/LiftOver.html

you could use the UCSC chain files and map your SNP back to GRCh38 http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/

ADD COMMENT

Login before adding your answer.

Traffic: 1924 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6