I need to compute LD blocks in hapmap CEU samples containing some SNPs. Genotype data in PLINK format were used.
ftp://ftp.ncbi.nlm.nih.gov/hapmap/ge.../plink_format/
HaploView failed to generate some block outputs, and inconsistency exists between Gabriel blocks and 4 gamete blocks.
java -jar ~/bin/Haploview.jar -n -pedfile snplist.ped -map snplist.map -blockoutput ALL -ldcolorscheme RSQ -png
Any suggestions on corrections or other methods?
Thanks a million!
ftp://ftp.ncbi.nlm.nih.gov/hapmap/ge.../plink_format/
HaploView failed to generate some block outputs, and inconsistency exists between Gabriel blocks and 4 gamete blocks.
java -jar ~/bin/Haploview.jar -n -pedfile snplist.ped -map snplist.map -blockoutput ALL -ldcolorscheme RSQ -png
Any suggestions on corrections or other methods?
Thanks a million!