Overview

With this task the PL values of the vcf are adjusted. The adjusted PL can either be provided directly or calculated internally with one of the estimation tasks.

Parameters

• vcf: specify the vcf for which the PL should be adapted
• newPLs: Provide a file with the adjusted PL's directly. The file must contain a header and the following 7 columns: sequencing batch, minimum depth, maximum depth, and the three new PL values
• errorRates: Provide a file with the genotyping error rates estimated with one of the estimation tasks. Column 1 and 2 are the depth interval for the error estimates, column 3 is the amount of genotypes in a given class, column 4 is the overall error, column 5 is homozygous error, column 6 is hetero error.
• errorModel: By default, an overall error rate is estimated as well as error rates for homozygous and heterozygous genotypes. In order to adjust the PL's using the overall error rate specify errorModel=1 (default) and for using the separate ones specify errorModel=2.

Output

• outname: change the output prefix. Default = prefix of vcf file

Usage example

./tiger task=adjustPL vcf=example.vcf.gz errorRates=example_errorRates.txt model=1 verbose