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Due to the way sequence variants are generated, in some cases variants at distance 2 with indels may be generated multiple times and the resulting values may be inaccurate.
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I was wondering if someone could explain why STAR is not left aligning these C insertions in this CC region (all the insertions are C's as well). Thanks for the help
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We've encountered some unexpected behaviour at a position where many of the samples have a deletion, and so have null genotype calls in the VCF file. Could you please advise?
The position is Spike …
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The option to have indels considered as missing data and not as a 5th characters is likely to be requested by many users. Then is the question of how to deal with missing data: I think that we should …
jflot updated
4 years ago
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Hi,
I am viewing some aligned reads on IGV as well as programmatically examining the cigar strings in my region of interest. I noticed not all the insertions/deletions present as indicated by the cig…
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At the moment we use pre-calculated values for SpliceAI, that only look at "all possible substitutions (snv), 1 base insertions
and 1-4 base deletions (indel) within genes"
We had a potential splice …
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Hello all,
For viral sequencing, often reference assembly is used to obtain the viral genome. In this case, it is useful to call a consensus sequence from the alignment. For Illumina data, this is …
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Not much Nanopore data has been run using the pipeline, so it's hard to say how appropriate the default parameters are for these data vs Illumina. However, some suggestions based on the [`setDadaOpt`]…
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Hey,
I have the following simplified vcf file (_"test_record.vcf"_)
```
##fileformat=VCFv4.2
##contig=
##FORMAT=
##ALT=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
1 1000000 . A .…
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![image](https://github.com/user-attachments/assets/edca4c8b-60a9-4f44-be37-9149a001425e)