Currently, we are updating the pipeline to support human genome build37, detail refers to bioinformatic wiki
As of today: Aug. 23rd, 2011, I have got both bwa59_b37_v1 and bwa59_b37_v4 running. The major difference between these two are the samtools version. Therefore, we want to validate the result before releasing to the full-speed realignment projects.
A few item to check as metrics
1. SVA concordance check (via master exome project)
2. Average coverage
3. LiftOver variants back to Build36 and compare the gain and lost
4. For Liz’s sample meta001, will check both genome and exome sample. And look for the “indel” that was missing at some samtools version (.1.7?)
SVA concordance project
1. Location: /home/jl407/project_2011/updatePipeline/SVA_concordance_check/
2. topstrand file (b36): /nfs/sva01/SequenceAnalyses/TopStrandFiles/Epigen_-_Round_4__Belgium_1-6__8-04-08_FinalReport_TopStrand_made_jan_26_2011.csv
3. topstrand file (b37):/home/jl407/svnroot/bioinfoDev/jyli/utils/B37_Epigen_-_Round_4__Belgium_1-6__8-04-08_FinalReport_TopStrand_made_jan_26_2011.csv
3. GWAS-ID: BEP282
Error with SVa concordance check,
Genome browser IDX file [gb2] is missing!Genome browser cannot be loaded.
??
Errors:
Genome browser IDX file [gb2] is missing!Genome browser cannot be loaded.