PMC:5985360 / 4537-5595
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5985360","sourcedb":"PMC","sourceid":"5985360","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5985360","text":"Sequence Data\nWe retrieved whole-genome-sequence data from 2,504 individuals in the 1000 Genomes Project,25 320 individuals in the African Genome Variation Project,26 and 108 individuals from Qatar.27 As previously detailed by the 1000 Genomes Project, a three-stage approach was used to establish phased haplotypes: (1) given array-based genotype data and family information, SHAPEIT2 was used to estimate a scaffold of long-range phased haplotypes, (2) a combination of Beagle and SHAPEIT2 was used to jointly analyze the long-range phased haplotypes and di-allelic variants, and (3) MVNcall was used to place multi-allelic and structural variants onto the haplotype scaffold.25 The average switch error rate was 0.56%, and the average distance between phasing errors was 1,062 kb.25 For comparison, the length of the β-globin locus, including the locus control region, is 67 kb. All data were accessed with VCFtools version 0.1.14.28 We assessed linkage disequilibrium in the 1000 Genomes Project data by using the --hap-r2 function for phased haplotypes.","divisions":[{"label":"title","span":{"begin":0,"end":13}}],"tracks":[{"project":"2_test","denotations":[{"id":"29526279-26432245-2046634","span":{"begin":105,"end":107},"obj":"26432245"},{"id":"29526279-25470054-2046635","span":{"begin":164,"end":166},"obj":"25470054"},{"id":"29526279-26728717-2046636","span":{"begin":198,"end":200},"obj":"26728717"},{"id":"29526279-26432245-2046637","span":{"begin":678,"end":680},"obj":"26432245"},{"id":"29526279-26432245-2046638","span":{"begin":783,"end":785},"obj":"26432245"},{"id":"29526279-21653522-2046639","span":{"begin":934,"end":936},"obj":"21653522"}],"attributes":[{"subj":"29526279-26432245-2046634","pred":"source","obj":"2_test"},{"subj":"29526279-25470054-2046635","pred":"source","obj":"2_test"},{"subj":"29526279-26728717-2046636","pred":"source","obj":"2_test"},{"subj":"29526279-26432245-2046637","pred":"source","obj":"2_test"},{"subj":"29526279-26432245-2046638","pred":"source","obj":"2_test"},{"subj":"29526279-21653522-2046639","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ec93ad","default":true}]}]}}