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Hello, I wonder how do you create the vcf file?
1. For example, how do deepvariant produce the value of QUAL of each variant?
2. I see you use p_error while calculating the GQ? What's the p_error…
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Add a column with the number of individuals who have a ceratin genotype (0/1 vs 1/1, and maybe 0/0 if gVCF)
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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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We currently have a folder called `delete_me` in the modules repo.
This contains a wide range of files that have been deposited, mostly for specific modules.
It is NOT included in the README file, …
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Hi~
In the last days, I tried to use kage to genotype my population, but it won't work well, please help me take a look:
'''
kage genotype -i 2/PN2_SNP -r data_tmp/CRR493563 -t 16 --average-cov…
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Hi,
I am currently running smoove on manta outputs and wanted to know if smoove genotypes based on lumpy or does it only consider the existing genotyping generated by manta?
Thank you!
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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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```shell
./graphtyper genotype ~/data1/References/human/bowen/Homo_sapiens_assembly38.fasta --sam=NA12878/alignment/NA12878.alt_bwamem_GRCh38DH.20150718.CEU.low_coverage.bam --region=chr21 --threads=…
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We're trying to use SNParcher on some fairly large genomic datasets at the moment (2000 + individuals), and I am anticipating a lot of slow-down at genotyping steps. I was wondering if it's possible t…
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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…