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Dear developers,
When running mtCOJO I am facing an error I have problems to solve.
My code:
Accepted options:
--bfile /home/all_snps
--mtcojo-file /home/mtCOJO/mtcojo_summary_data.list.txt
…
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MCHap can report haplotypes that have not been called in the posterior mode of any individual (i.e., and allele count of 0). This is necessary when reporting statistics over the posterior (such as the…
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Hi,
Thank you for the great package. I encountered a strange error when using mat_gen_dist() function. The function works well with my genind object (transformed from genlight using gl2gi() functi…
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Hello,
When I run strelka2 somatic variants calling with "--reportEVSFeatures", I got variants vcfs containing values of "TumorSampleAltAlleleFraction". Those values are very close to "Somatic all…
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Enabling InitialPrevalence by constructing genomes from distributions of allele frequencies as specified in the config
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**Is your feature request related to a problem? Please describe.**
Currently we selected markers for SNP array/chip at random, meaning that we can get similar distribution of allele frequencies as fo…
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Thank you so much for making this repo. The B allele frequencies and logr values are important features for our studies but the version of our GTC files is 3, which means we cannot get those two featu…
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Hello Folks,
Strelka2 is our go to caller for standard somatic variant calling. It works well down to about 5% AF. We'd like it to work with our ctDNA variant calling where the read depth exceeds…
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The new variant annotation data is available:
- JSON: `gs://ot-team/dsuveges/variant_index_new_json` (7.72 GiB)
- Parquet: `gs://ot-team/dsuveges/variant_index_new` (1.01 GiB)
- New data availa…
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Would it be possible to include the STRider Import for allele frequencies as present in the main EuroForMix package into EFMrep as well?