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Current variant calling/Mutect parallelization only uses major contigs right now. But, with B38, this would drop ALT contigs
Not dropping them makes sense, but in general variant calling likely needs…
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Hi,
I was trying to use IsoPhase do call SNPs from the Pacbio Isoseq data for a single sample. However, when I run the `select_loci_to_phase.py `with all the files required, I was keeping getting 0…
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Deepvariant creates a summary report which I would like us to save permanently in Housekeeper.
The report contains the relative counts of variants inside a sample. This could, later on, be used for…
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We are performing somatic variant calling in tumour-only mode where we call variants with both Mutect2 (GATK version 4.1.2.0) and Vardict-java. We have noticed that Mutect2 calls adjacent phased indel…
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Hi,
I'm just wanting to check in regarding how to obtain an all-sites VCF using snpArcher. From what I can tell, I just need to add the -all-sites flag to the GenotypeGVCFs command in the following…
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On some datasets (Peromyscus), processes that are spawned to call variants with GATK sometimes get locked or do not spawn a new GATK process, resulting in only 1 process being used to call variants. T…
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If the BAQ calculation is a significant compute fraction of a variant calling pipeline can we get a faster turnaround by threading that BAQ calculation? (be it in `samtools calmd`, `samtools mpileup`,…
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I'm working with a library that has a variant class with non-explicit constructors for basic types like `Variant(bool)` and `Variant(const char *)`. After adding sol3 `sol_lua_get/push/check()` functi…
RDaac updated
1 month ago
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Hi @grbot
I see that the mitochondrial variant calling pipeline excluded "Align the unmapped BAM file with the reference aligned BAM and shifted reference aligned BAM" step described in [mt-varian…