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 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`

`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