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Single sample calling with multi-sample output?

Hi,

Is there a way do single sample variant calling but have the output directly in a mutli-sample vcf? We now do single sample calling and after that combine the vcf file to a multi-sample vcf file. The creates really large intermediary files (with all reference positions) and takes much longer than multi-sample calling.

We have some NGS data from a non standard experiment with non standard samples, were we are looking at small differences between the samples. We chose to do single sample variant calling because we don't want the the data from one sample to influence the calls in the other. And we are not sure what the assumptions for multi-sample calling are and if they apply for our experiment.

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