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I propose we do the following:
**Delete:**
"width" - this is the width of the locus in the ref genome. Not needed as it can be easily computed from start/end.
"normal" - this is the text version …
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I used intervar to predict mutations and found no pathogenic entries, what went wrong?
In addition, I found that some loci are contradictory, such as the situation that PM1 and BS1 are satisfied at…
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Comparing
https://github.com/PacificBiosciences/trgt/blob/main/repeats/pathogenic_repeats.hg38.bed
to
https://github.com/broadinstitute/str-analysis/blob/main/str_analysis/variant_catalogs/varia…
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We moved to rankscore, but raw scores are used in ACMGv4 in PP3_supporting
Check out if any others are used
We should also run eg REVEL as a tool instead of dbNSFP
If not on the short variants then…
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STRs as a new variant type to include in analysis.
We are making use of Small variants and SVs (see #372... 😞), but CPG already runs STRipy reports on all samples. We can use that as a source of in…
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hi @egor-dolzhenko
Regarding the Repeat definition files, I only saw files related to hg38 in the link you provided. Does this software not support the analysis of data for hg19/GRCh37? Or are there…
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[InStrain enables population genomic analysis from metagenomic data and rigorous detection of identical microbial strains](https://www.biorxiv.org/content/10.1101/2020.01.22.915579v1)
Coexisting mi…
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Hi Sigve
Thanks for another awesome framework. We (@umccr) are very much interested to incorporate this into our reporting.
I have looked at the github repo/code and tested it locally - it works…
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Hello there,
Is there a guide for prioritizing outliers? i.e. focusing on STRs with a Z-score >10? How do we filter from all the background noise?
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I have called a bunch of samples with straglr and merged the (chrom, start, end, motif) beds into one unified bed. I would like to use this merged bed to genotype each sample again. Sometimes differen…