SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA


Name (Type)

vcfs (file)

One or a list of uncompressed VCF file


fasta (file)

Reference genome VCF was generated against


snpeff_results (file)

Results from snpEff in txt format (Optional)


gff (file)

GFF file corresponding to reference genome fasta (Optional)


allele_freqs (boolean)

Whether to include the percentage of reads a given allele is
present in in the SNP table.

genotype_quality (integer)

Minimum GATK genotyping threshold threshold of which a SNP call
falling under is ‘discarded’

coverage (integer)

Minimum number of a reads that a position must be covered by to be

homozygous_freq (integer)

Fraction of reads a base must have to be called ‘homozygous’

heterozygous_freq (integer)

Fraction of which whereby if a call falls above this value, and lower
than the homozygous threshold, a base will be called ‘heterozygous’.

gff_exclude (file)

file listing positions that will be ‘filtered’ (i.e. ignored)



Name (Type)

versions (file)

File containing software versions


bam (file)

Sorted BAM/CRAM/SAM file


full_alignment (file)

Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls


info_txt (file)

Information about the run


snp_alignment (file)

A fasta file of just SNP positions with samples only


snp_genome_alignment (file)

A fasta file of just SNP positions with reference genome


snpstatistics (file)

Some basic statistics about the SNP calls of each sample


snptable (file)

Basic SNP table of combined positions taken from each VCF file


snptable_snpeff (file)

Input file for SnpEff


snptable_uncertainty (file)

Same as above, but with lower case characters indicating uncertain calls


structure_genotypes (file)

Input file for STRUCTURE


structure_genotypes_nomissing (file)

Alternate input file for STRUCTURE


json (file)

Summary statistics in MultiQC JSON format



GPL >=3

MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA. License on Github repository.