from hg18 to GRCh38 reference human genome [closed]

Question

Closed. This question does not meet Stack Overflow guidelines. It is not currently accepting answers.

---

This question does not appear to be about programming within the scope defined in the help center.

Closed 6 years ago.

Improve this question

Does anyone know if it is possible to convert SNP coordinates from Hapmap database to the new reference genome GRCh38. UCSC doesn't have the liftover yet ready. Any suggestions?

Answer 1

As was linked in the BioStars answer, NCBI offers a remapping tool that will translate positions from one reference genome to another. UCSC also offers a similar tool, LiftOver, which has a downloadable version as well.

However, as I discovered years ago, these tools do not always succeed in remapping your coordinates, and sometimes produce incorrect results. You should take all output from these tools with a grain of salt. Bottom line, you should only assume your original coordinates are the correct ones, and try to work with the corresponding reference genome build.

Answer 2

The UCSC liftover tool as mentioned above can work most of the time https://genome.ucsc.edu/cgi-bin/hgLiftOver

However, there might be repetitive pieces which may make the liftover tool confused.

An alternative way is to map the sequences (fasta/fastq) onto the new hg38 genome using bowtie to get coordinates.