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Revision as of 19:39, 15 June 2014
, 19:39, 15 June 2014→Motivation
This wiki page details some standard Indel analyses which hopefully can help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
This wiki page details some standard Indel analyses which hopefully can help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
This wiki page details some standard Indel analyses for the sequencing workshop in the example indel data set.
== Anatomy of all.genotypes.bcf ==
== Anatomy of all.genotypes.bcf ==
vt view -H all.genotypes.bcf.
vt view -H all.genotypes.bcf.
The file generated from the indel calling is a binary version [[http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2 BCFv2.1]] of the Variant Call Format (VCF). BCFv2.1 is more efficient to process as the data is already stored in computer readable format on the hard disk. It is however not necessarily more compact than VCF4.2 especially when the format fields are rich in details.
The header is as follows:
The header is as follows:
