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VCF2Genome

A tool to create a draft genome file out of a GATK VCF file

Download via GitHub Releases or via Bioconda.

Author: Alexander Herbig herbig@shh.mpg.de (v0.84), Alexander Peltzer (v0.90+).

Contact Alexander Peltzerpeltzer@shh.mpg.de for questions regarding the tool or via GitHub and/or open a ticket here.

Basic Usage description

Help message

You can see a help when running the tool with -h. This generates the following help message:

Option "-draft" is required
 -draft VAL                 : draft contains Ns where no call can be made. RefMod contains reference calls instead at
                              these positions.
 -draftname DRAFT_SEQ_NAME  : Name of the draft sequence.
 -h                         : Display this help information and exit. (default: true)
 -in VAL                    : input VCF file
 -minc MIN_COVERAGE_FOR_SNP : Minimum coverage / reads confirming the call.
 -minfreq MIN_SNP_FREQUENCY : Minimum fraction of reads supporting the called nucleotide.
 -minq MIN_QUAL_SCORE       : Minimum quality score. For UG: Phred scaled quality score. For HC genome quality score.
 -ref VAL                   : reference genome in FastA format
 -refMod VAL                : More precise uncertainty encoding. N: Not covered or ambiguous. R: Low coverage but looks
                              like Ref. a,c,t,g (lower case): Low coverage but looks like SNP.
 -uncertain VAL             : Special 1234 encoded FastA output.

Example: java -jar VCF2Genome.jar -draft VAL -draftname DRAFT_SEQ_NAME -in VAL -minc MIN_COVERAGE_FOR_SNP -minfreq MIN_SNP_FREQUENCY -minq MIN_QUAL_SCORE -ref VAL -refMod VAL -uncertain VAL

Option documentation

Example call

java -jar VCF2Genome.jar -draft my_output_genome.fasta -draftname "My_Fancy_Genome_Name" -in my_input.vcf -minc 5 -minfreq 0.8 -minq 30 -ref myreference_genome.fasta -refMod output.refMod -uncertain 1234_output.fasta

-draft

Name of the output file to which the FastA genome sequence should be written. Contains Ns where no call can be made.

-draftname

Name of the draft sequence inside the FastA file (header of the FastA entry that is created).

-in

Name of the input VCF file in VCF4.0/4.1 format.

-minc

Minimum coverage / reads confirming the call required.

-minq

Minimum quality threshold used for filtering the calls.

-minfreq

Minimum fraction of reads supporting the called nucleotide.

-ref

Reference genome used in FastA format.

-refMod

Path to refMod format output file. This contains a more detailed output encoding than just including N at unclear positions. Useful for further investigation of some sites for example. N: Not covered or ambiguous. R: Low coverage but looks like Reference call. a,c,t,g (lower case): Low coverage but looks like SNP.

-uncertain

Path to uncertainty encoded output file in a special 1234 format for some downstream tools.

Additional comments

VCF Compatibility

Note that this tool was written a couple of years ago for reconstructing genomes from GATK UnifiedGenotyper VCF output files. It may work with other genotypers providing the same kind of VCF4.0/VCF4.1 format, but might not work well with data originating for example from GATK HaplotypeCaller. The tool requires an EMIT_ALL_SITES compatible VCF input file.

SNP/Indel handling

This tool is currently unable to handle indels properly due to the index handling procedure in the software itself. SNPs are fine.