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## Describe the issue
VEP fails with the error message "Can't call method "each_seq" on an undefined value at \ensembl-vep/Bio/EnsEMBL/Variation/TranscriptHaplotype.pm line 451, line 75759."
Imme…
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Hii!
I am trying to use parallel singer and it returns the following error:
/singer/singer-0.1.7-beta-linux-x86_64/convert_long_ARG.py", line 118, in
main()
/singer/singer-0.1.7-beta-linux-…
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Hi,
I'm running minimac4 on a phased VCF file with a 1000 Genomes reference, all chromosomes combined.
I prepared the reference like this:
1) Downloaded the 1000 Genomes Phase 3 (V5):
> wget f…
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Hello there,
I just used [GRIDSS](https://github.com/PapenfussLab/gridss) to call SVs and want to use the resulting VCFs to calculate Fst with `--weir-fst-pop` and get a pairwise matrix with `--012…
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I'd like to see how to generate mutation and lineage reports using only *.vcf as an input. The commercial lab that provides our county wastewater sequencing services provides a *.vcf , but doesn't pro…
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### Description of feature
This time I tried to look through issues and code. ;)
As far as I can see, sarek does not do any kind of variant decomposition, which (if coupled with normalization) can…
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Hi everyone, I'm new to coding and Snakemake so I needed some help.
Unfortunately, I've encountered a problem when I tried the `bash run.sh all_harmonize_target_genotypes` step when trying to use VC…
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hello,When I used data with Visium for fresh-frozen from https://www.10xgenomics.com/cn/datasets/fresh-frozen-visium-on-cytassist-human-breast-cancer-probe-based-whole-transcriptome-profiling-2-standa…
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Dear authors,
I have read your paper and want to detect the cross sample contamination. But the description of this software is poor. Can you make it clear and write a turuor please.
Best,
Lian…
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I get the vcf file form cnv_facets
I use the WGS data
I wonder How can I get the segment data from the vcf data
especially the column of number of probe