SNPsnap

Many users have requested a command-line version of SNPsnap. Running SNPsnap on the command-line would allow for great flexibility/customization and no restriction on the job size (number of input SNPs) so you never have to wait if the SNPsnap server is down. Unfortunately we do not have time to develop the command-line tool, so instead we are looking for SNPsnap users to help us out. The task is modify the main SNPsnap engine (snpsnap_query.py) to run using the SNP annotation database files located on the SNPsnap download site.
If you would like to help out, please reach out to us contact us or submit a pull-request on the SNPsnap GitHub repo

We frequently experience high load on the SNPsnap web-server. Although we are happy about the demand and use of SNPsnap, it unfortunately means that the server crashes from time to time. When the SNPsnap server has crashed, it returns the page 'Internal server error (code 500)' after you've submitted your job. If you get this error message, you will usually have to wait one or two hours (but sometimes up to 24 hours) before the server has rebooted and is online again. If the server crashes all running jobs are lost (and you will not receive an email notifying you about the job completion).
You should only contact us if the problem persists for more than two days. We are currently looking into solving this problem by 1) emailing users if their jobs failed because of server overload; and 2) upgrading the SNPsnap server to better support the usage load. We are sorry about the inconvenience that this downtime may cause our users.
To help minimize the downtime, we ask our users to be mindful about the number of jobs they submit simultaneously. Do not submit multiple jobs containing tens of thousands input SNPs as this is likely to crash the server.

SNPsnap is not able to match X chromosome SNPs. Input X chromosome SNPs are still accepted but they will be excluded during the matching algorithm (exclusion mark: SNP_genetic_properties_corrupted_in_data_base). We are sorry about the inconvenience this may cause our users.

SNPsnap now offers to download SNPsnap's annotation database. Check it out here

SNPsnap have undergone a major update. Here is the list of new features:

• SNPsnap is now based on 1000 Genome Phase 3 data. The old Phase 1 data is no longer supported.
• Super populations (European, EUR; East Asian, EAS; West African, WAFR) are added to allow more specific SNP matching based on your study population.
• X-chromosome SNPs included.
• Geneset updated to GENCODE genes.
• New SNPsnap annotation features: MAF, HGNC symbols, distance to nearest protein coding gene, flag for SNP within gene and more.
• SNPsnap now uses the lightning fast PLINK 1.9 for clumping input SNPs.

We hope you enjoy the new and improved version! Please do not hesitate to give us feedback.

Checking indepence of SNPs have never been easier: we have integrated an option for reporting the independence of your input SNPs. You can adjust the threshold of clumping (both LD and physical distance) after selecting the checkbox Report input loci independence. This will generate the file input_snps_clumped.txt where researches can inspect the clumping in more details.

SNPsnap now accepts rs-numbers as SNP input. In addition SNPsnap generates the file input_snps_identifer_mapping.txt to ease the mapping to/from chromosomal coordinates and rs-numbers.

SNPsnap now includes a matching bias calculation to determine differences between the mean genetic properties of input and matched SNPs.
This helps the user to balance the trade-off between requesting a large number of matched SNPs while avoiding systematic differences between input and matched SNPs.

SNPsnap now supports a new exclusion feature Exclude HLA SNPs.
Enabling this option will exclude all input SNPs mapping to the HLA region (chr 6 25Mb-35Mb) in both input and matched SNPs.

The team behind SNPsnap is excited to announce that SNPsnap is now online.
We strongly encourage you to provide feedback for any improvements to the website or SNP matching parameters.