Current Methods:
All using phased variant information from ENCODE experiment ENCSR053AXS.
1) Create custom linear reference genome using vcf2diploid (http://alleleseq.gersteinlab.org/tools.html) maternal and paternal custom fasta files are generated for each chromosome. Need to concatenate and re-align reads for select datasets to each (paternal and maternal).
2) Create custom graph reference genome using vg (https://github.com/vgteam/vg). Create genome using vg construct, index genome using vg index, and map genome using vg map.
Current Methods: All using phased variant information from ENCODE experiment ENCSR053AXS.
1) Create custom linear reference genome using vcf2diploid (http://alleleseq.gersteinlab.org/tools.html) maternal and paternal custom fasta files are generated for each chromosome. Need to concatenate and re-align reads for select datasets to each (paternal and maternal).
2) Create custom graph reference genome using vg (https://github.com/vgteam/vg). Create genome using vg construct, index genome using vg index, and map genome using vg map.