Description

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

vcfs:file

One or a list of uncompressed VCF file

*.vcf

meta2:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

fasta:file

Reference genome VCF was generated against

*.{fasta,fna,fa}

meta3:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

snpeff_results:file

Results from snpEff in txt format (Optional)

*.txt

meta4:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

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’.

meta5:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

gff_exclude:file

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

*.vcf

Output

name:type
description
pattern

full_alignment

meta:file

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

.fasta.gz

fullAlignment.fasta.gz:file

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

.fasta.gz

info_txt

meta:file

Information about the run

.txt

info.txt:file

Information about the run

.txt

snp_alignment

meta:file

A fasta file of just SNP positions with samples only

.fasta.gz

snpAlignment.fasta.gz:file

A fasta file of just SNP positions with samples only

.fasta.gz

snp_genome_alignment

meta:file

A fasta file of just SNP positions with reference genome

.fasta.gz

snpAlignmentIncludingRefGenome.fasta.gz:file

A fasta file of just SNP positions with reference genome

.fasta.gz

snpstatistics

meta:file

Some basic statistics about the SNP calls of each sample

.tsv

snpStatistics.tsv:file

Some basic statistics about the SNP calls of each sample

.tsv

snptable

meta:file

Basic SNP table of combined positions taken from each VCF file

.tsv

snpTable.tsv:file

Basic SNP table of combined positions taken from each VCF file

.tsv

snptable_snpeff

meta:file

Input file for SnpEff

.tsv

snpTableForSnpEff.tsv:file

Input file for SnpEff

.tsv

snptable_uncertainty

meta:file

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

.tsv

snpTableWithUncertaintyCalls.tsv:file

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

.tsv

structure_genotypes

meta:file

Input file for STRUCTURE

.tsv

structureGenotypes.tsv:file

Input file for STRUCTURE

.tsv

structure_genotypes_nomissing

meta:file

Alternate input file for STRUCTURE

.tsv

structureGenotypes_noMissingData-Columns.tsv:file

Alternate input file for STRUCTURE

.tsv

json

meta:file

Summary statistics in MultiQC JSON format

.json

MultiVCFAnalyzer.json:file

Summary statistics in MultiQC JSON format

.json

versions

versions.yml:file

File containing software versions

versions.yml

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