Galaxy |

Convert Affymetrix (version 1.9)

Probeset annotation file:

Apt-probeset genotype summary file:

Apt-probeset genotype snp-posteriors file:

Apt-probeset genotype report file:

Apt-probeset genotype confidences file:

Apt-probeset genotype calls file:

Choose the source for the reference genome:

Select reference genome:

Output apt-probeset-genotype gender estimate?:

Append version and command line to the header?:

Select format for output:

This tool converts Affymetrix genotype calls and intensity files to VCF format.

Required options

Probeset annotation file - probeset annotation file produced by the sequencing run.

Apt-probeset genotype summary file - apt-probeset genotype summary file produced by the sequencing run.

Apt-probeset genotype snp-posteriors file - apt-probeset genotype snp-posteriors file produced by the sequencing run.

Apt-probeset genotype report file - apt-probeset genotype report file produced by the sequencing run.

Apt-probeset genotype confidences file - apt-probeset genotype confidences file produced by the sequencing run.

Apt-probeset genotype calls file - apt-probeset genotype calls file produced by the sequencing run.

Choose the source for the reference genome - select a reference genome from your history or one installed into your local Galaxy environment by a data manager tool.

Other options

Output apt-probeset-genotype gender estimate - output apt-probeset-genotype gender estimate into an additional dataset.

Append version and command line to the header - append version and command line to the header of the output VCF dataset.

Select format for output - select one of uncompressed/compressed VCF/BCF.