1) There is now a different parameter for sample name (-sn), sample file (-sf) or sample expression (-se). The unexpected behavior of the previous implementation was way too tricky to leave unchecked. (if you had a file or directory named after a sample name, SV wouldn't work)
1b) Fixed a TODO added by Eric -- now the output vcf always has the samples sorted alphabetically regardless of input (this came as a byproduct of the implementation of 1)
2) Discordance and Concordance now work in combination with all other parameters.
3) Discordance now follows Guillermo's suggestion where the discordance track is your VCF and the variant track is the one you are comparing to. I have updated the example in the wiki to reflect this change in interpretation.
4) If you DON'T provide any samples (-sn, -se or -sf), SelectVariants works with all samples from the VCF and ignores sample/genotype information when doing concordance or discordance. That is, it will report every "missing line" or "concordant line" in the two vcfs, regardless of sample or genotype information.
5) When samples are provided (-sn, -se or -sf) discordance and concordance will go down to the genotypes to determine whether or not you have a discordance/concordance event. In this case, a concordance happens only when the two VCFs display the same sample/genotype information for that locus, and discordance happens when the disc track is missing the line or has a different genotype information for that sample.
6) When dealing with multiple samples, concordance only happens if ALL your samples agree, and discordance happens if AT LEAST ONE of your samples disagree.
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Integration tests:
1) Discordance and concordance test added
2) All other tests updated to comply with the new 'sorted output' format and different inputs for samples.
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Methods for handling sample expressions and files with list of samples were added to SampleUtils. I recommend *NOT USING* the old getSamplesFromCommandLineInput as this mixing of sample names with expressions and files creates a rogue error that can be challenging to catch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6072 348d0f76-0448-11de-a6fe-93d51630548a
BinomialCumulativeProbability was reformatted to follow the now standard parameter order.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6057 348d0f76-0448-11de-a6fe-93d51630548a
Added stratification by lane to ReadBackedPileup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6046 348d0f76-0448-11de-a6fe-93d51630548a
a) If we were selecting SNPs or Indels and there was one of each at the same location, only whichever one was pulled first was processed.
b) Fixed logic error when selecting Mendelian Violations: if that option was used it wasn't possible to combine with other options.
c) Fixed logic error when using -disc option: you shouldn't parse genotypes to check whether a site is present or not because a vcf can be sites-only and this is slow.
d) Made -disc option work in the same way as other options: variants are now selected from "variant" track all the time, and variants which are not in disc track are kept. Inverse logic (keep disc variants not present in "variant") is confusing and prevents users from combining with different options.
With these changes it is now possible to ask for example "Give me all indels which are Mendelian Violations, not in dbsnp and present in these samples" which was not possible before.
Integration tests covering the above are forthcoming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6027 348d0f76-0448-11de-a6fe-93d51630548a
VariantEvalWalker now passes a pointer to itself to the Stratefication setVariantEvalWalker (and assoc. get method) so that stratefications can look at VEWalker variables to obtain information necessary for their calculations, like the list of eval samples. This is a better interface, in my opinion, than the current approach of extending the base abstract Stratefication to include an initialize function that has all arguments necessarily for any Strat.
JEXL expressions now provide access to the VariantContext vc object itself, so you can write JEXL's that directly use VariantContext and associated functions from the command line.
ExomePostQC Queue script now creates a byAC eval using the new strat, and no longer produces a byAF file (as this was not exact, and lead to strange punctile behavior when actual AF quantization was out of sync with fix quantization of AF strat.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6015 348d0f76-0448-11de-a6fe-93d51630548a
b) Bug fix: multiallelic indel records where not being treated properly by VQSR because vc.isIndel() returns false with them. Correct general treatment for now is to do (vc.isIndel()||vc.isMixed()).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5973 348d0f76-0448-11de-a6fe-93d51630548a
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