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

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

java remap liftover eutils
• 4,663 views • link
updated by Ram Ram • written by burcakotlu • burcakotlu

Thank you Pierre.

Meanwhile I have used NCBI remap.

But I will try your suggestions too.

Maybe then I may have further questions.

Burçak

• 0 views • link
written by burcakotlu • burcakotlu

1 answer

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/

• 1 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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