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Hello, Brad!
Thanks for the great pipeline!
Currently among read-depths CNV callers only CNVkit is supported in bcbio. In our experience ERDS and CNVNator perform better than CNVkit. What would …
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I was able to replicate the users error with GATK4.1.1.0 and the latest build on Nov21. The users data is on the FTP as livinlrg_Problem_Interval.
Running SelectVariants on the same data generates…
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Via @mjsteinbaugh:
@naumenko-sa I'm looking into using bcbio for RNA-seq variant calling at the moment. Are the current recommendations still VarDict and MuTect2 for cancer cells? I'd like to add s…
roryk updated
4 years ago
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Hi,
Since recently my bcbio jobs crash on a SGE cluster because the jobs run into the default job memory limit.
By default all jobs on our cluster, unless overwitten, have these memory limits:
…
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Hi,
It seems that gatk4.0 has removed indel quality recalibration function.
I need indel quality to use Mutect2. Is there any tool I can use to recalibrate indel quality?
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Hello,
I've been searching through all the threads for choosing correct VCF file. I have 23 Process matched controls and 3 Tumor samples , where I want to investigate allele specific copy number …
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In GATK3 sometimes in gross indels the genotype would be called for the NON_REF allele. This may be improved in GATK4.1 with the new QUAL model, but it's worth putting some checks, i.e. after https:/…
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selected articles from https://github.com/broadinstitute/gsa-unstable/wiki are relevant to gatk4 and should be migrated
the task here is to review the wikis and select the relevant ones and migrate t…
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Hi,
First I filter snp.raw.vcf with `VariantFiltration` command below:
`gatk-4.1.2.0/gatk --java-options "-Djava.io.tmpdir=/tmp/" VariantFiltration -R genome.fa -V snp_rmnan.raw.vcf --filter-expr…
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User Request:
> Samtools is multithreaded, we should be able to speed up converting to a bam file and sorting
We use `samtools view` in a gitc-bw-mem-samtools tool:
https://github.com/bespin-work…