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notes.md

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Avro stuff

http://metaclaws.com/2013/01/27/automatically_load_avro_schemas_that_reference_other_schemas/

ANN, LOF, NMD fields

http://snpeff.sourceforge.net/SnpEff_manual.html

SnpEff adds 'LOF' and 'NMD' tags to INFO fields (column 8 in VCF format). LOF and NMD tags have the following format: Gene | ID | num_transcripts | percent_affected

Interpretation of ANN field cancer sample relies on 'Allele' sub-field. Just as a reminder, ANN field has the following format: ANN = Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS_WARNINGS_INFO

release to bintray

  • change the version in versions.sbt
  • sbt publish