Hi, I am looking for time efficient variant caller for pooled samples ( samples are mixed first and DNA extraction is carried out) to identify the SNPs and small Indels. It will be nice if it is recent and well cited.
Thank you.
With regards,
Tanushree Tiwari
GATK and VarScan perform exceptionally well! You might find attached articles useful.
Article Evaluation of variant detection software for pooled next-gen...
Article Next Generation Sequencing of Pooled Samples: Guideline for ...
Thank you so much Vijay.
Yes GATK is undoubtedly very good but the time it takes is too much for 50 pooled samples. I am trying LoFreq from the first reference attached and i find it useful and interesting.
With regards,
Tanushree
Google Brain Team recently released DeepVariant. We implemented a reproducible version that was submitted to NF-Core (https://lifebit.page.link/UW58).
We also made it available in Lifebit (https://lifebit.page.link/os1m) if you want to try it with example parameters.
In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format.
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