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Hello, I have a question concerning phasing using pedigree information :
I have a vcf of 23 individuals, and their respective bam files. They are either full sibs or not related but the parents are …
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When I run an MK test on the corBra test data it runs fine, but when I run it on my data I am getting KeyError: '*'. I'm running multiple chromosomes separately, the error occurs in most but not all. …
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I am benchmarking the tools for balancing "compression and accessibility" of genotypes, and I have encountered several issues while trying to use GVC. These issues may prevent fair comparisons with th…
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I generated vcf's from MANTA then annotated them using AnnotSV tool. then tried running vcf2circos tool i get this error :
>> $ vcf2circos --input output.vcf --options Static/options.json --output ou…
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Dear team,
very useful method that I'm running already for genotyped data, but also wanted to run on VCF files containing imputed data.
When running the command (Julia 1.8.5):
`ordinalgwas(@f…
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Hello, I have problem about the sorted and duplicated position when conduct QUILT_prepare_reference.R
My code is: (according to UILT_hla_reference_panel_construction.Md)
oneKG_vcf_name=CCDG_14151_B0…
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Hi,
I'm running cactus-pangenome with diploid data as input: two files per individual (14 fasta files), named as described in the docs. For 6 of the 7 individuals the vcf output is diploid, but one i…
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We need to review what https://nf-co.re/sarek can do to determine:
- if it could be used as is
- if it could be used with modifications
- if we'd rather extract and replicate some functionality h…
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Hi.
I am an absolute beginner in this aspect. When I run the script with a vcf input file, I get this error. Error: Failed to open data.vcf.gz. (--vcf expects a complete filename; did you forget '.…
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I have a large scale dataset of WXS .g.vcfs , I do not have the original FASTA files. I would like to genotype these .g.vcfs into vcfs. These vcfs will be used in downstream applications. The issue is…