mal10mal13 - christianparobek/cambodiaWGS GitHub Wiki
First, looked at Michele's LID paper to get Mal10 and Mal13 coordinates: MAL10:688956 and MAL13:1718319.
Next, made a BED file (mal10mal13.bed) with these variants:
Pf3D7_10 688955 688956
Pf3D7_13 1718318 1718319
Then performed a liftOver on my laptop, since the liftOver binary I found works for Ubuntu, not RedHat:
./liftOver beds/mal10mal13.bed chainfile/2to3.liftOver beds/mal10mal13_liftover.bed beds/mal10mal13_lifttrash.bed
Got out these results:
Pf3D7_10_v3 688956 688957
Pf3D7_13_v3 1718287 1718288
Searched for these in split VCFs using IGV. Note, include the outliers with CP2. Also, make sure to use split VCF files that have SN084 -> SN094. I had to remake these files in this folder. Having some trouble with CP3 (not sure what it is, but only 18 of the expected 20 samples are showing up in the VCF file after I split), but here's what I have for the time being: