Changes

* --chip-mix is turned on for estimating contamination or swap using sequence+array method, if the external genotype file is provided in the VCF

* --chip-mix is turned on for estimating contamination or swap using sequence+array method, if the external genotype file is provided in the VCF

* --self is turnd on : The default option does not try to compare the sequence reads to identify the best matching individual (which is possible with --best option). It only compares with the external genotypes from the same individual to the sequenced individual.

* --self is turnd on : The default option does not try to compare the sequence reads to identify the best matching individual (which is possible with --best option). It only compares with the external genotypes from the same individual to the sequenced individual.

* --maxDepth 20 ise used without --precise option : The default option is intended for whole genome low coverage sequencing. For the targeted exome sequencing, --maxDepth 1000 and --precise is recommended.

* --maxDepth 20 is used without --precise option : The default option is intended for whole genome low coverage sequencing. For the targeted exome sequencing, --maxDepth 1000 and --precise is recommended.

* --ignoreRG is not a default, but a recommended option, when you want to check the contamination for the entire BAM rather than examining each read group separately. This option will increase the computational efficiency especially in the case whether the sequence reads are multiplexed across many sequencing runs.

* --ignoreRG is not a default, but a recommended option, when you want to check the contamination for the entire BAM rather than examining each read group separately. This option will increase the computational efficiency especially in the case whether the sequence reads are multiplexed across many sequencing runs.

 

== Interpreting output files ==

== Interpreting output files ==