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Hi,
Thanks for developing this nice tool.
I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of them, and call variants. T…
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### Description of the bug
I am running a single sample, and ended up assigning the same ID for both "sample" and "case" columns in the input samplesheet.
This crashes in a step where Tomte attemp…
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📌 Explain the Request
Fasta files entering the allele calling workflow need to only keep the original identifier and need to have no newline characters / spaces after the header or sequence.
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Hi,
I saw Ploidetect requires the definition of snp array. Is that used for allele-specific CNV calling?
If that is, can I replace the array by germline SNV sites or some common snp from dbSNP?
…
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# 1. Purpose
The cg/wgMLST allele calling pipeline will be used for calling alleles from genomic sequence data.
*Note: This is an in-development description of this pipeline.*
# 2. Input
#…
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Hello,
I've noticed that when I re-genotype a VCF using Sniffles2, the allele depth ended up being 0 for an insertion I'm looking at, while before re-genotyping this AD was 12, and the reads with t…
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Hi! Thanks for providing a python-based version of CARLIN pipeline. We want to modify the arguments to run on our own sequencing data and reference from a different experiment protocol. However, I can…
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Hi
I have simulated some haploid data with Illumina error rates and ancient DNA data. It is ~25x coverage.
I wanted to see how the damage influences heterozygosity/genotype calls.
I noticed that …
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Hello, I am having trouble getting bcftools to call the ALT allele with 61 DP4 depth, it instead is only showing the REF call with 0 DP4 read depth.
The ALT call is correctly identified in the 'bc…
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I have encountered the following error. I have tried both with out without --save_output_as_bam. It didn't help. I also ensured sufficient memory (256G) is available.
Thank you!
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