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Some discussion in https://github.com/pystatgen/sgkit/pull/647#discussion_r686015457
As pointed out by @jeromekelleher it's interesting to look at the main [init](https://github.com/pystatgen/sgkit…
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freebayes -f /share/home/shh/download/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa -iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 6 ${souporcell_out}minitagged_sorted.bam
##fileformat=VCFv4.1
#…
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Dear Adam,
After reading the manual it sounded like a minor mis-specification of theta doesn't affect the estimate of rho that much.
But I hope to understand the proper method for setting theta i…
melop updated
7 years ago
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Hi,
Can RUTH handle chromosome X? There isn't a mention of it in the manuscript, but the program accepts parameters for sex chromosomes. When I try to load a BCF file containing X-chromosome SNPs, …
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Hello @jonassibbesen,
Just reaching out for a bit of assistance
Out of 33,462 candidate SVs called with Manta, I have successfully genotyped 26,606 SVs. To compare the relative frequency of SV ty…
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### Description of feature
Add VCF to JSON conversion with certain filter to use for the visualization of the SVs
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We want to be able to structure a set of data items that is generated by particular study, so that the data can collectively be can be linked to Statements about it, provenance information supporting …
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Dear Jared,
Thank you again for the great software.
I am having some issues with one variant not being called correctly from Nanopolish.
In that position, the reference has a T, while my sampl…
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Hello,
I have HLA genotype data in the form of (dummy example):
| A | A | B | B | DRB1 | DRB1 |
| ----------- | ----------- | ----------- | ----------- | ----------- | ----------- |
| 02:01 …
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Hi,
I have two VCF files and want to calculate genotype concordance on a per samples basis. The two VCF files contain only the genotype values that were imputed based on two different approaches an…