I want to increase accuracy in the variants using multiple variants calling tools such as Varscan, GATK, Samtools(vcftools),BreakDancer. Is there any pipeline which provide output by combining the results of each individual tools?
From my experience in the clinical genetics scene in the UK, sampling reads at 'random' from your BAM file (picard DownsampleSam)and then calling variants on each 'sub BAM' with samtools mpileup piped into bcftools call (and then obtaining a consensus listing of all variants) is enough to find all true-positives that can possibly be found. On many occasions, GATK and other tools will 'miss' variants, for whatever reasons. It is erroneous to believe that simply running multiple tools on the same sample, or repeating the same sample in the lab, is enough.
A loose benchmark: 1000 Genomes variants were identified by merging the calls from multiple variant callers. However, using the method above, it was very easy to find all variants in 1000 Genomes that had already been found (and there was even evidence that the consortium had missed variants that should have been reported).
If you have unmatched samples, you might be interested in appreci8, an approach that combines 8 variant callers and introduces a custom filtering strategy that was trained on an extensive number of datasets to improve sensitivity.