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Revision as of 11:04, 27 June 2014
, 11:04, 27 June 2014→Preparing Input Files
Check the contents of the VCF file using the following command.
Check the contents of the VCF file using the following command.
zless $OUT/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz
zless ${OUT}/thunder/chr22/ALL/thunder/chr22.filtered.PASS.beagled.ALL.thunder.vcf.gz
=== Phenotype Information ===
=== Phenotype Information ===
Phenotype information is prepared in PED format commonly used in other GWAS software such as MERLIN or PLINK.
Phenotype information is prepared in PED format commonly used in other GWAS software such as MERLIN or PLINK.
less $IN/assoc/seqshop.ped
less ${SS}/assoc/seqshop.ped
The first several line should look like below.
The first several line should look like below.
