David Benjamin
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Activity overview
Latest activity by David Benjamin-
David Benjamin commented,
On all hardware in my experience Mutect2's I/O time is very small compared to CPU time. I don't think you need to worry about I/O contention. We parallelize WGS bams 100 ways all the time without...
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David Benjamin commented,
Regarding 2), restricting your intervals to just the force-calling alleles (i.e. -L ${GGA_path}/vcf/${sample}_GGA_union.vcf.gz) might cause problems. Can you try applying interval padding (I would...
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David Benjamin commented,
@Fia It is totally normal for FilterMutectCalls to filter 90% or more of Mutect2 variant calls. Mutect2 is designed to be very permissive and naive, leaving almost all the responsibility for filte...
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David Benjamin commented,
When a sample has no read coverage near a force-calling allele Mutect2 can't emit it because the GATK engine skips over the region. Is that the case for your SNPs that were not called? Some discre...
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David Benjamin commented,
M Carta I'm not sure this is the root of the issue but the lack of sequence dictionary lines eg ##contig=<ID=chr2,length=242193529> in the header of your "manual" VCFs worries me a bit. How about...
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David Benjamin commented,
Melcar Collodetti A few comments on the workflow, which I hope will be helpful: The -L argument in GetPileupSummaries should usually be the same vcf file as the -V argument. We recommend using the...
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David Benjamin commented,
Probably 1-4 days for code review and merging into the master branch, followed by roughly a month between minor releases.
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David Benjamin commented,
Luka Culibrk This new PR: https://github.com/broadinstitute/gatk/pull/8717 removes germline events from the accounting of the ECNT annotation and should fix the unfortunate interaction between the...
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David Benjamin commented,
Jyoti Mridha This looks like a custom-made filtering pipeline. It does not resemble our best practices. The hard filtering most likely does very little since it is filtering based on several anno...
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David Benjamin commented,
Yes, that will work fine.