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Pileup to VCF (version 2.2)

Source File:

Set column positions for non-standard pileup:

Minimum Base Quality:

Don't consider a read if the base call quality is below this threshold

Minimum Coverage Depth:

Any position below the threshold will be omitted from the resulting VCF

Minimum Frequency of a Specific Allele:

If an allele does not meet the minimum frequency it will be omitted from the resulting VCF.

Allow Multiple Alleles for a Position?:

Multiple alleles may be output in the VCF if the allowable frequency is below 0.5, otherwise only one will be reported

Only report SNPs, not indels:

Report DP and SAF with read coverage of:

The reported read voverage depth: DP, and the calculation of specific allele frequency (SAF) of variants

The VCF ID:

The VCF output will use this as the ID field value

Pileup to VCF converts the output of a pileup tool to a VCF representing any alleles that surpass a user specified frequency, optionally presenting multiple alleles for a given position if the allele frequency is set below 0.5. This tool assumes that any filtering for base call quality and mapping quality has been done in previous processing.