Data Visualizsations
Linkage Disequilibrium
Example haplotype block (11:750000-799999).
LD block plots were generated for chromosome 11 regions of Medaka in overlapping 50 kb windows shifted by 25kb each time. We used a perl wrapper script (LDmaps.pl) to generate ped files, and then run Haploview in -nogui mode i.e.
java -jar ~/bin/Haploview.jar -nogui -pedfile file.ped -memory 10000 -dprime -blockoutput GAB
Various files are available
- The compressed vcf file and its tabix index.
- LDmaps.pl the perl wrapper used to run the analysis.
- vcf_to_ped_convert.pl a perl wrapper to make ped from vcf from the 1000 genomes project. N.B. Tabix is required to be in your path for vcf_to_ped_convert.pl.
- A set of sample LD block images. Haplotype blocks in the 16 medaka founders were called using Haploview using the default parameters for the method described by Gabriel et al. (2002). The plots show the LD of pairs of SNPs by squares joining the two SNPs via the diagonal and are colour coded as described for the standard LD color scheme such that pairs of SNPs in LD at D’ = 1 are colored blue at LOD< 2 and red at LOD >= 2, whilst those with D’ <1 are white at LOD < 2 and shades of red/pink at LOD >= 2.
chr1 160000-180000
chr11 100000-149999
chr11 125000-174999
chr11 150000-199999
chr11 175000-224999
chr11 200000-249999
chr11 225000-274999
chr11 250000-299999
chr11 275000-324999
chr11 300000-349999
chr11 325000-374999
chr11 350000-399999
chr11 375000-424999
chr11 400000-449999
chr11 425000-474999
chr11 450000-499999
chr11 475000-524999
chr11 500000-549999
chr11 525000-574999
chr11 550000-599999
chr11 575000-624999
chr11 600000-649999
chr11 625000-674999
chr11 650000-699999
chr11 675000-724999
chr11 700000-749999
chr11 725000-774999
chr11 750000-799999
chr11 775000-824999
chr11 800000-849999
chr11 825000-874999
chr11 850000-899999
chr11 875000-924999
chr11 900000-949999
chr11 925000-974999
chr11 950000-999999
chr11 975000-1024999
