Description

SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA

Input

Name
Description
Pattern

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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'.

0 ()

1 ()

Output

Name
Description
Pattern

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0 ()

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0 ()

0 ()

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Tools

multivcfanalyzer Documentation

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

doi: 10.1038/nature13591License: GPL >=3
Authors