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I am looking to have both SNV called and non SNV's in the same vcf for downstream analyses.
My temporary workaround at the moment is to run the tool twice, once with the reference to generate the …
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### Is your feature related to a problem?
Yes
Maintaining consistency of analyses in a reasonable timeframe.
### Describe the solution you'd like
I've ran the full pipeline on samples, but forgot …
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### Description of feature
`spliceai_21_scores_raw_snv_-v1.3-.vcf.gz` contains scores for chr21, and not those overlapping the testdata.
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Hello,
I'm new to Palimpsest and I'm trying to preprocess and annotate input data but I have an error that I don't understand. I tried with other data and it worked. Any suggestion ?
![session i…
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Example to reproduce on a local demo:
### On SNV variants page, this filter works:
And you get 3 variants which have likely benign clinsig
### This filter also works
You get no v…
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### Description of feature
At the moment everything is published, including intermediary files. We might have to think of more long-term solutions for some of these, but a fix in the near future is n…
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Hi,
If I called a heterozygous SNP with short read, then phase it with long-read.
But in long-read, at the same position is not a heterozygous SNP,
may be it is a homozygous SNP or no SNP.
What wi…
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### Contact Details
chiwonchung98@gmail.com
### What happened?
I've been tinkering with this pipeline for a few days but I cannot get it to work. I'm fairly new to Snakemake so I'm not exactly sure…
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```Insertion(variant=Variant(contig='16', start=17549386, ref='A', alt='G', reference_name='GRCm38'), transcript_name=Lrrc74b-204, transcript_id=ENSMUST00000232637, effect_description=p.310insR)```
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Hi qing,
when i used the command:
giremi -f Sus_scrofa.Sscrofa10.2.dna.toplevel.fa -l H.txt -p 1 -s 0 -o H.RNAE.lst brain.sort.rmdup.bam,
I got the problem like that:
[mpileup] 1 samples in 1 inp…