|
|
| Line 1: |
Line 1: |
| IZJu5O Thanks for sharing, this is a fantastic post. Great. | | IZJu5O Thanks for sharing, this is a fantastic post. Great. |
|
| |
|
| == File Formats ==
| | zn9fdv Thanks for the blog post.Thanks Again. Cool. |
| | |
| | |
| Results should be shared as plain text files, with the following variable names:
| |
| | |
| {| width="800" border="1" class="prettytable"
| |
| |-
| |
| | width="200" | '''''variable name'''''
| |
| | '''''description'''''
| |
| |-
| |
| | '''SNPID'''
| |
| | SNP ID as rs number
| |
| |-
| |
| | '''chr'''
| |
| | chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.<br>
| |
| |-
| |
| | '''position'''
| |
| | physical position for the reference sequence (indicate build 35/36 in readme file)
| |
| |-
| |
| | '''coded_all'''
| |
| | coded allele, also called modeled allele (in example of A/G SNP in which AA=0, AG=1 and GG=2, the coded allele is G)
| |
| |-
| |
| | '''noncoded_all'''
| |
| | the other allele
| |
| |-
| |
| | '''strand_genome'''
| |
| | + or -, representing either the positive/forward strand or the negative/reverse strand of the human genome reference sequence; to clarify which strand the coded_all and noncoded_all are on
| |
| |-
| |
| | '''beta'''
| |
| | beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available<br>
| |
| |-
| |
| | '''SE'''
| |
| | standard error of beta estimate, to at least 5 decimal places -- “NA” if not available<br>
| |
| |-
| |
| | '''pval'''
| |
| | p-value of test statistic, here just as a double check -- “NA” if not available
| |
| |-
| |
| | '''AF_coded_all'''
| |
| | allele frequency for the coded allele -- “NA” if not available<br>
| |
| |-
| |
| | '''HWE_pval'''
| |
| | exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed<br>
| |
| |-
| |
| | '''callrate'''
| |
| | genotyping callrate after exclusions
| |
| |-
| |
| | '''n_total'''
| |
| | total sample with phenotype and genotype for SNP
| |
| |-
| |
| | '''imputed'''
| |
| | 1/0 coding; 1=imputed SNP, 0=if directly typed
| |
| |-
| |
| | '''used_for_imp'''
| |
| | 1/0 coding; 1=used for imputation, 0=not used for imputation
| |
| |-
| |
| | '''oevar_imp'''
| |
| | observed divided by expected variance for imputed allele dosage
| |
| |}
| |
| | |
| ''Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.''
| |
| | |
| [[Category:Analysis Guidelines]]
| |
| [[Category:Analysis]]
| |