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apeltzer / VCF2Genome

A tool to create a draft genome file out of a GATK VCF file
GNU General Public License v3.0
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No EMIT_ALL_SITES required anymore #2

Open apeltzer opened 7 years ago

apeltzer commented 7 years ago

Improve VCF2Genome to be able to read a normal VCF file (not EMIT_ALL_SITES, rather EMIT_CONFIDENT_SITES or EMIT_DEFAULT)

apeltzer commented 7 years ago

http://gatkforums.broadinstitute.org/wdl/discussion/4017/what-is-a-gvcf-and-how-is-it-different-from-a-regular-vcf

https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php#--emitRefConfidence

https://samtools.github.io/hts-specs/VCFv4.2.pdf

apeltzer commented 7 years ago

use gVCF, introduce mutations in FastA string and annotate at which position you introduced the mutation properly in a separate indelstats file.

Attention: Once changed, we have to keep the offset in a pointer and state this instead of the current position (!) otherwise, this ruins our indelstats file (or state both for example, makes it easier for reads to get a feeling what we mean here....