a) Updating for posterity original scripts for VQSR project consensus (snp and indel) so that they use newest GATK syntax (also they were not run in the end). b) New scripts for redoing indel GL's, jobs are split per sample and per chromosome.

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Another script (PhaseIndelRedoCombining.scala) does the combining of all pieces - not the best solution, but best for development/debugging to have two separate entities.
c) Experimental walker to assess GL concordance of two callsets - just accumulates squared error between each sample and site GL's and outputs at the end.
d) Another one-off to fill a callset of given GL's with greedy genotypes (genotype that maximizes PL) to have more meaningful metrics and QC of a given GL file.

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Guillermo del Angel 2011-12-19 16:50:52 +01:00

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