Description

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

Input

Name (Type)
Description
Pattern

vcfs (file)

One or a list of uncompressed VCF file

*.vcf

fasta (file)

Reference genome VCF was generated against

*.{fasta,fna,fa}

snpeff_results (file)

Results from snpEff in txt format (Optional)

*.txt

gff (file)

GFF file corresponding to reference genome fasta (Optional)

*.gff

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
reported

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)
(Optional)

*.vcf

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

bam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

full_alignment (file)

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

.fasta.gz

info_txt (file)

Information about the run

.txt

snp_alignment (file)

A fasta file of just SNP positions with samples only

.fasta.gz

snp_genome_alignment (file)

A fasta file of just SNP positions with reference genome

.fasta.gz

snpstatistics (file)

Some basic statistics about the SNP calls of each sample

.tsv

snptable (file)

Basic SNP table of combined positions taken from each VCF file

.tsv

snptable_snpeff (file)

Input file for SnpEff

.tsv

snptable_uncertainty (file)

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

.tsv

structure_genotypes (file)

Input file for STRUCTURE

.tsv

structure_genotypes_nomissing (file)

Alternate input file for STRUCTURE

.tsv

json (file)

Summary statistics in MultiQC JSON format

.json
maintainer
Github user jfy133
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

multivcfanalyzer
GPL >=3

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

github.com/alexherbig/MultiVCFAnalyzer 10.1038/nature13591