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Famrvtest

1,223 bytes added, 14:13, 20 August 2014
VCF File
tabix -p vcf -f input.vcf.gz ## this command will generate input.vcf.gz.tbi
* Even with the presence of VCF file, PED/DAT files are still needed for covariates and phenotypes.
 
=== Group File for Gene-level Tests===
* Grouping methods are only necessary for gene-level tests.
* With --groupFile option, you can specify particular set of variants to be grouped for burden tests.
* The group file must be a tab or space delimited file in the following format:
GROUP_ID MARKER1_ID MARKER2_ID MARKER3_ID ...
* MARKER_ID must be in the following format:
CHR:POS_ALLELE1/ALLELE2
* An example group file is:
PLEKHN1 1:901922_G/A 1:901923_C/A 1:902088_G/A 1:902128_C/T 1:902133_C/G 1:902176_C/T 1:905669_C/G
HES4 1:934735_A/C 1:934770_G/A 1:934801_C/T 1:935085_G/A 1:935089_C/G
 
===Group Info from Annotated VCF File===
If --groupFile option is '''NOT''' specified, ''''famrvtest''' will look for an annotated vcf file as blue print for variants to group. Users are also allowed to generate a vcf file based on the superset of variants from pooled samples, and annotate outside RAREMETAL. Then, annotated vcf file can be used as input for RAREMETAL for gene-level meta-analysis, or group files can be generated based on the annotated vcf file. Detailed description of these options are [[Rare-Metal#Group_Rare_Variants_from_Annotated_VCF|'''available''']].
== Example Command Line ==
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