Add option to generate VCF output for all methods

bergmanlab / mcclintock

Meta-pipeline to identify transposable element insertions using next generation sequencing data

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Closed cbergman closed 9 years ago

cbergman commented 10 years ago

Since we are calling variants we should consider adding support to generate VCF files for each method in addition the BED files.

see VCF format specification here: http://vcftools.sourceforge.net/specs.html
Retroseq already generates output in VCF format
need to think about best way to represent TSD and non integer based predictions
need to understand how to incorporate reference insertions into VCF (currently Retroseq doesn't include)

cbergman commented 9 years ago

There is some precedent for annotating CNVs in VCF here: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/VCF%20%28Variant%20Call%20Format%29%20version%204.0/encoding-structural-variants
However, as we want to encode information about reference insertions as well as non-reference insertions, VCF may not be suitable for our purposes