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vcf2pca: src/./include/Eigen/src/Core/DenseCoeffsBase.h:427: Eigen::DenseCoeffsBase::Scalar& Eigen::DenseCoeffsBase::operator()(Eigen::Index) [with Derived = Eigen::Matrix; Eigen::DenseCoeffsBase::Sca…
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**1. What were you trying to do?**
```
vg giraffe --output-format gam --gbz-name $vg.gbz --minimiser-name $autoindex.min --dist-name $autoindex.dist -f $R1 -f $R2 -t $threads $reference.fa $vcf.gz…
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@sandve, I am working on reconstructing a haploid haplotype using the imputed genotypes from KAGE. Currently, I am using the following commands:
```bash
kage index -r MHC-CHM13.ref.fa -v MHC_49-M…
gsc74 updated
2 months ago
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Hi Simon, I'm curious about your thoughts regarding how filtering a VCF file for LD and phasing might influence the results of ABBA-BABA tests. I have played around with different filtering parameters…
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**What is your question?**
@eblerjana I am working on reconstructing a haploid haplotype using the imputed genotypes from PanGenie. Currently, I am using the following commands:
```bash
PanGenie …
gsc74 updated
2 months ago
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During the filtering steps regions will be filtered out but their ids remain in the final output vcf file
example for 80K ARV1|ENSG00000173409.14|EH38E2873165_fwd_tile1-1
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Processed 598000 variants in 151.979secs，Program received signal SIGSEGV, Segmentation fault.I first suspected that it was a problem with my vcf file because I did not filter for missing sites when fi…
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Good afternoon,
I'm writing this to report an issue I've been having while trying to do a test run for graphtyper's genotype_sv command.
I ran 2 sv-callers: Manta and Smoove on 50 samples and th…
ghost updated
1 month ago
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Hi, Thank you for making INSurVeyor program.
Unfortunately, when I ran this program, the following problem occurred.
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Remapping DC for chr4_GL000008v2_random
DC remapped in 6 [s…
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Trying to extract a vcf out of an annotated file (single sample). The number of entries is smaller than the ones in gui (excel, tsv are correct).
This is true when reports are obtained from gui as w…