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Hello,
First, I want to express my gratitude for developing xTEA.
I am encountering an issue while using xTEA’s case-control mode to identify somatic transposon (specifically Alu) insertions. Ba…
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Hi,
Thanks for a great tool. I am playing around with genotyping amplicon data from Nanopore sequencing. I can get Straglr to call certain STRs but not others, and I wonder if I need to do somethin…
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It might be nice to be able to genotype on multiple SNP sets in a single run. I'm specifically thinking of pileupcaller here, not sure how it would apply to other genotypers, but:
Currently, the re…
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Expected Behavior
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add a linking table to phenome schema with the following structure:
table name: allele_marker
colu…
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Greetings!
Do you have any plans on implementing the genotyping of the variants? Or if you recommend tool that could genotype the VCF output of nanomonsv.
Cheers!
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Dear all,
I am evaluating possibilities for genotyping hundreds of fungal genomes and came across the Maast paper. Would you see any particular problem in applying Maast to fungal or eukaryotic gen…
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Hi
I completed the genotyping of all samples (the previous error was not resolved, so I replaced one of the samples). After merging them, I conducted quality control. Unfortunately, the genotyping…
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BAMfiles probably need to be QNAME sorted (rather than coordinate sorted) when splitting them
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Hi, I'm trying to genotype an SV VCF with Delly and getting this error:
```
Error: Delly genotyping requires local SV assembly (INFO/CONSENSUS) and breakpoint (INFO/CONSBP) introduced in delly v1.1.…
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Found bam file: /home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/10x_multiomics/CellRanger_ARC/1016715_pool3_hg38/outs/gex_possorted_bam.bam for genotyping.
Wed Mar 20 12:38:37 CET 2024: Fo…