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

How should I deal with tandem repeat?



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    Bhanu Gandham

    From the IGV screenshot I am not able to tell what  the two tracks are. Can you please provide that info?

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    David Benjamin

    This site doesn't look so bad to me.  The PCR slippage model relies on the empirical fact the indel error rate for STRs is usually lower than 1 in 10 reads.  For most Illumina sequencing this is, in fact, overly conservative.  The fact that the deletion is seen in 10 out of 38 tumor reads and in no normal reads leads me to trust it.  The fact that you also see some insertion errors doesn't mean much.  If your sequencing for some reason is more prone to PCR slippage at STRs than the assumptions of FilterMutectCalls you may increase the slippage rate parameter at the cost of many false negatives.

    I also don't see a good reason to call this a mapping error because the errors are all at the STR site.  Mapping artifacts almost always exhibit a bunch of scattered substitution errors.

    The STRQ cap of 93 follows the cap on qual scores in the SAM/BAM spec.

    I also notice a lot of non-default parameters in FilterMutectCalls, all set to very strict values.  These parameters should only be adjusted if one has a very good reason to do so.  Likewise, I recommend running Mutect2 and FilterMutectCalls with their default settings for STRs.

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