David Benjamin
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Activity overview
Latest activity by David Benjamin-
David Benjamin commented,
Rose Gold Unfortunately this tool is not one we officially support. It's basically a one-off custom tool we wrote for CGA way back. However, there is an unmerged PR that seems to have the missing...
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David Benjamin commented,
Nicolas Loucheu ISmolicz It's possible Mutect2 is discarding this as a possible germline event before it gets to assembly and genotyping. First, you should use the af-only-gnomad VCF from the GATK...
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David Benjamin commented,
ISmolicz We have not resolved the issue. Sometimes assembly-related problems like this can be resolved by using the -linked-de-bruijn-graph option.
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David Benjamin commented,
ISmolicz The bamout shows the reads after they are trimmed to a fit a local assembly region. The abrupt cutoff is simply the boundary of this assembly region.
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David Benjamin commented,
Mutect2 can write the output VCF and VCF index to arbitrary paths, either local files or buckets. The stats file, however, can only be written locally. When we run Mutect2 on the cloud, eg in the...
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David Benjamin commented,
Laurent MANCHON This is confusing because FilterMutectCalls doesn't remove variants from the output. It only applies FILTER tags. Are the variants within the $ONCO_BED intervals file? As a check...
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David Benjamin commented,
I'm glad that worked. You didn't miss anything. We have never compiled a set of best practices for amplicon data.
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David Benjamin commented,
The -bamout argument needs to be followed by a path to the bamout file. The argument parser is seeing "-stride" as the value of the -bamout argument, and then sees "20" as a standalone positional ...
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David Benjamin commented,
It looks like a lot of reads start at exactly the same position in the original bam. The GATK's default downsampler restricts to at most 50 reads starting at each position. When start positions a...
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David Benjamin commented,
Hi Shivangi, That's about the difference I would expect. Using a matched normal will have more of an impact. Regards, David