Description

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

Input

name:type
description
pattern

meta{:bash}

:map

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

vcfs{:bash}

:file

One or a list of uncompressed VCF file

*.vcf

meta2{:bash}

:map

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

fasta{:bash}

:file

Reference genome VCF was generated against

*.{fasta,fna,fa}

meta3{:bash}

:map

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

snpeff_results{:bash}

:file

Results from snpEff in txt format (Optional)

*.txt

meta4{:bash}

:map

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

gff{:bash}

:file

GFF file corresponding to reference genome fasta (Optional)

*.gff

allele_freqs{:bash}

:boolean

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

genotype_quality{:bash}

:integer

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

coverage{:bash}

:integer

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

homozygous_freq{:bash}

:integer

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

heterozygous_freq{:bash}

: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{:bash}

:map

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

gff_exclude{:bash}

:file

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

*.vcf

Output

name:type
description
pattern

full_alignment{:bash}

meta{:bash}

:map

Groovy Map containing sample information

fullAlignment.fasta.gz{:bash}

:file

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

.fasta.gz

info_txt{:bash}

meta{:bash}

:map

Groovy Map containing sample information

info.txt{:bash}

:file

Information about the run

.txt

snp_alignment{:bash}

meta{:bash}

:map

Groovy Map containing sample information

snpAlignment.fasta.gz{:bash}

:file

A fasta file of just SNP positions with samples only

.fasta.gz

snp_genome_alignment{:bash}

meta{:bash}

:map

Groovy Map containing sample information

snpAlignmentIncludingRefGenome.fasta.gz{:bash}

:file

A fasta file of just SNP positions with reference genome

.fasta.gz

snpstatistics{:bash}

meta{:bash}

:map

Groovy Map containing sample information

snpStatistics.tsv{:bash}

:file

Some basic statistics about the SNP calls of each sample

.tsv

snptable{:bash}

meta{:bash}

:map

Groovy Map containing sample information

snpTable.tsv{:bash}

:file

Basic SNP table of combined positions taken from each VCF file

.tsv

snptable_snpeff{:bash}

meta{:bash}

:map

Groovy Map containing sample information

snpTableForSnpEff.tsv{:bash}

:file

Input file for SnpEff

.tsv

snptable_uncertainty{:bash}

meta{:bash}

:map

Groovy Map containing sample information

snpTableWithUncertaintyCalls.tsv{:bash}

:file

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

.tsv

structure_genotypes{:bash}

meta{:bash}

:map

Groovy Map containing sample information

structureGenotypes.tsv{:bash}

:file

Input file for STRUCTURE

.tsv

structure_genotypes_nomissing{:bash}

meta{:bash}

:map

Groovy Map containing sample information

structureGenotypes_noMissingData-Columns.tsv{:bash}

:file

Alternate input file for STRUCTURE

.tsv

json{:bash}

meta{:bash}

:map

Groovy Map containing sample information

MultiVCFAnalyzer.json{:bash}

:file

Summary statistics in MultiQC JSON format

.json

versions{:bash}

versions.yml{:bash}

: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