modules/multivcfanalyzer

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

vcfancient DNAaDNASNPGATK UnifiedGenotyperSNP table

https://github.com/nf-core/modules/[...]/modules/nf-core/multivcfanalyzer

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 gzipped or 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`
`:map`

Groovy Map containing sample information

`*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`
`:map`

Groovy Map containing sample information

`*info.txt`
`:file`

Information about the run

.txt

`snp_alignment`

`meta`
`:map`

Groovy Map containing sample information

`*snpAlignment.fasta.gz`
`:file`

A fasta file of just SNP positions with samples only

.fasta.gz

`snp_genome_alignment`

`meta`
`:map`

Groovy Map containing sample information

`*snpAlignmentIncludingRefGenome.fasta.gz`
`:file`

A fasta file of just SNP positions with reference genome

.fasta.gz

`snpstatistics`

`meta`
`:map`

Groovy Map containing sample information

`*snpStatistics.tsv`
`:file`

Some basic statistics about the SNP calls of each sample

.tsv

`snptable`

`meta`
`:map`

Groovy Map containing sample information

`*snpTable.tsv`
`:file`

Basic SNP table of combined positions taken from each VCF file

.tsv

`snptable_snpeff`

`meta`
`:map`

Groovy Map containing sample information

`*snpTableForSnpEff.tsv`
`:file`

Input file for SnpEff

.tsv

`snptable_uncertainty`

`meta`
`:map`

Groovy Map containing sample information

`*snpTableWithUncertaintyCalls.tsv`
`:file`

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

.tsv

`structure_genotypes`

`meta`
`:map`

Groovy Map containing sample information

`*structureGenotypes.tsv`
`:file`

Input file for STRUCTURE

.tsv

`structure_genotypes_nomissing`

`meta`
`:map`

Groovy Map containing sample information

`*structureGenotypes_noMissingData-Columns.tsv`
`:file`

Alternate input file for STRUCTURE

.tsv

`json`

`meta`
`:map`

Groovy Map containing sample information

`*MultiVCFAnalyzer.json`
`:file`

Summary statistics in MultiQC JSON format

.json

`versions_multivcfanalyzer`

`${task.process}`
`:string`

The name of the process

`multivcfanalyzer`
`:string`

The name of the tool

`multivcfanalyzer -h | head -n 1 | cut -f 3 -d " "`
`:eval`

The expression to obtain the version of the tool

`versions_tabix`

`${task.process}`
`:string`

The name of the process

`tabix`
`:string`

The name of the tool

`tabix -h 2>&1 | grep Version | cut -f 2 -d " "`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`multivcfanalyzer`
`:string`

The name of the tool

`multivcfanalyzer -h | head -n 1 | cut -f 3 -d " "`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`tabix`
`:string`

The name of the tool

`tabix -h 2>&1 | grep Version | cut -f 2 -d " "`
`:eval`

The expression to obtain the version of the tool

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