Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

low af variant with contamination tag

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    Gökalp Çelik

    Hi Junfeng Jiang

    We would recommend you to check our paper for how we estimate whether a low frequency variant is a true variant or a contamination artifact

    https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf 

     

    The more the population allele frequency for a variant the highly likely that it may get filtered out as being a contaminant in other samples. If your sample was confirmed to carry this mutation in the tumor biopsy/or an alternate ctDNA sample from the same patient that was not used in the initial sequencing then you may want to recheck the way you include contamination filter for your ctDNA samples as they show variants with even lesser fractions inside, therefore contamination filter may not be ultimately useful for the purpose of selecting variants as a screening result of ctDNA sequencing. I consulted our team about this question and they may post more insights later. 

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    Junfeng Jiang

    yes, I definetely read the contamination filter in the document and know the algorithm to calculate the probability of the contamination.

    Our statistics showed that the contamination score is always around 0.005, which will largely affect the variation selection, especially for those drug response ones.

    And it may be inappropriate to raise this question that any suggestions to reduce the contamination in experimental step?

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    Gökalp Çelik

    Hi again. 

    Contamination here could be partly due to index jumps and partly due droplet contamination during experimentation none of which could be easily get rid of especially when you are talking about levels of 0.005. 

    Our team suggests that for your purpose it may be better of not using this filter at all. 

    Regards. 

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