{"id":1152,"date":"2017-08-18T15:56:49","date_gmt":"2017-08-18T13:56:49","guid":{"rendered":"http:\/\/wp.unil.ch\/sgg\/?page_id=1152"},"modified":"2020-03-03T15:50:56","modified_gmt":"2020-03-03T14:50:56","slug":"summary-statistic-imputation-software","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/sgg\/program\/summary-statistic-imputation-software\/","title":{"rendered":"Summary Statistic Imputation software"},"content":{"rendered":"

This command-line software enables summary statistics imputation (SSimp) for GWAS summary statistics.<\/p>\n

The only input needed from the user are the GWAS summary statistics<\/strong>\u00a0and optionally a reference panel<\/strong><\/em> (if different from the 1000 Genomes) for LD computation.<\/p>\n

Download<\/span><\/strong><\/p>\n

The compiled binary file for linux<\/em>\u00a0and osx<\/em> can be downloaded from here<\/a>.<\/div>\n

Examples<\/strong><\/span><\/p>\n

ssimp --gwas gwas\/small.random.txt --ref ref\/small.vcf.sample.vcf.gz --out output.txt<\/code><\/p>\n

This will impute the Z-statistics, using a selected reference panel (see section above) and generate a file output.txt<\/em>, which stores the imputed summary statistics. The txt file assigned to--gwas<\/code>\u00a0contains at least the following columns: SNP-id, reference allele, risk allele, Z-statistic, and at least one row.<\/p>\n

Note that multiprocessing mode is not yet implemented, hence to speed up computation we recommend splitting up the job to smaller chromosomal chunks using<\/p>\n

ssimp --gwas gwas\/small.random.txt --ref ref\/small.vcf.sample.vcf.gz --out output.txt<\/code> --impute.range\u00a0<\/code><\/span>22:18000000-22:18100075<\/code><\/p>\n

Documentation<\/strong><\/span><\/p>\n

    \n
  1. Run ssimp with no arguments to see the [usage message<\/a>]<\/li>\n
  2. Check out [examples<\/a>]<\/li>\n
  3. Read the [detailed manual<\/a>] that contains information not present in the usage message.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    This command-line software enables summary statistics imputation (SSimp) for GWAS summary statistics. The only input needed from the user are the GWAS summary statistics\u00a0and optionally a reference panel (if different … <\/p>\n","protected":false},"author":970,"featured_media":0,"parent":15,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"class_list":["post-1152","page","type-page","status-publish"],"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages\/1152","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/users\/970"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/comments?post=1152"}],"version-history":[{"count":0,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages\/1152\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages\/15"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/media?parent=1152"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}