kage
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ivargr
Alignment-free genotyper for SNPs and short indels, implemented in Python.
Hi！ thanks for your advanced software！ : ) How can I determine the memory size required for indexing? I always get “not enough memory” when I run the `kage index`...
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...
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...
Hello, I am trying to install kage. Due to conflicts with packages, I am not able to install it. I first created a conda environment and installed python version 3.8...
Hi, I encountered an error while running the kage index, which seems to be an issue during the parsing of the VCF file. My input files were a chromosome from...
If I want to genotype SNPs, InDels and SVs, should I create two indexs, one for SNPs and InDels, and another for SVs, then run kage genotype twice?
Hi, I'm trying to run the indexing step of kage on my data set but I get the following error: `ValueError: zero-size array to reduction operation maximum which has no...
I am trying to test kage 0.11.14 but cannot for some reason kmer_mapper does not work. The command and error message: kmer_mapper map -b index_2548all_uncompressed.npz -f 210435_S26_L001_R1_001.fq -o kmer_counts Traceback...
Hello, Wondering if it's possible to build indexes for quick genotyping of low coverage samples ( ~2-5x ~1500+) from a set of samples generated at higher coverage (~500, 10-20x) for...
I just saw the preprint and KAGE looks like a promising alternative to GATK. Would it be possible to use KAGE to genotype ancient DNA samples? The golden standard at...