Bovine reference UMD_3.1 liftover
O'Sullivan, Niall
Proprietary
Hi there,
I have question regarding the bovine reference genome. I want to know if it is necessary to perform a liftover of reference data before I begin analysis . Previously I used Bostau UMD 3.1 and I would like to start using UMD 3.1.1.
Should the SNP co-ordinates be the same between the two builds?
The vcf files with the regions of interest are located here and align to UMD 3.1: http://gong_lab.hzau.edu.cn/Animal_ImputeDB/#!/download_cattle
Thanks in advance
Niall
Niall O’Sullivan, PhD
Genomics Research Specialist
R&D
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Luis Nassar
Hello, Niall.
Thank you for your interest in the Genome Browser.
Looking at the GenBank entry for this cow genome (https://www.ncbi.nlm.nih.gov/assembly/GCF_000003055.6/#/st) we see the following:
In June 2014 138 contigs were suppressed because they are contaminants, so the assembly name was updated to Bos_taurus_UMD_3.1.1, assembly GCA_000003055.4.
In November 2014 37 more contigs were suppressed because they are contaminants and two contigs (DAAA02065100 and DAAA02065112) were unsuppressed because they were determined to be Bos taurus. Therefore, a total of 173 contigs are suppressed. The assembly name remains Bos_taurus_UMD_3.1.1 but the assembly was incremented to GCA_000003055.5.
It is my understanding from that that the differences between 3.1 and 3.1.1 are only in the unplaced contigs. Meaning annotation coordinates on the primary chromosomes should all be identical. That being said, as we did not generate this genome and only host the 3.1.1 version, we cannot make any guarantees. You can also contact the submitters to clarify this information (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA32899/).
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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