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Hi,
I have created a pangenome using the minigraph-cactus pipeline in a manner very similar to how the HPRC created their pangenome (using T2T-CHM13 as the primary reference and including GRCh38 as…
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# Scratch pad
hs38 primary assembly of GRCh38 (incl. chromosomes, unplaced and unlocalized contigs) and EBV
hs38a hs38 plus ALT contigs
hs38DH hs38a plus decoy contigs and HLA genes (r…
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We want to handle `NONCOPY` states in partial ancestral haplotypes in the reference panel when running the LS Viterbi and forward-backward algorithms, for both the haploid and diploid cases.
I shou…
szhan updated
5 months ago
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I'm encountering a segmentation fault when running LongTR with phased BAM tags to genotype and phase TRs. Below are the details of the command used and the error message.
DIR=test_data
./LongTR --…
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Hi,
First of all, thanks a lot for developing Minimac4, it is a great tool.
I have an issue regarding recalculating (and replicating) Rsq (imputation quality) values. I am interested in this be…
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It seems there may be different views and practices regarding how we should specify deletion alleles ("^", "*", "_", "-",...) and start/stop coordinates (first base, base before, last base, base after…
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From my review of the code, we have:
1. `GenotypeGvcfs` first [merges overlapping variant contexts](https://github.com/broadinstitute/gatk/blob/master/src/main/java/org/broadinstitute/hellbender/tool…
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Dear Dr Kolmogorov,
I work with very strange genome of sea cucumber and could not get a mosaic haploid genome assembly. I tried some options (meta, keep-haplotypes, no-alt-contigs, tweaks from ONT re…
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Thank you for creating this valuable tool. We've found it to be the best for analyzing our data compared to other tools, but we've noticed a discrepancy in genotyping the KIR2DL5A/B genes. While other…
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**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6.1/docs/FAQ.md**:
Yes
**Describe the issue:**
I have processed around 30 samples albeit having some issues with GPU, pos…