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Hi all,
I am new to the field and I'd like to verify my variant calling pipeline using latest CHM13 as reference. I have the HG002v1.1.fasta here and I got the truth set v1.1.vcf from NIST.
> (ht…
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In the summary of the meta-analysis (below) there is a total tally of variants per category. However, this seems to be a bit of (error file reports many more variants that were not found in the refere…
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Hi there,
I'm using SAIGE v1.0.4 with conditional analysis. This works well when I have a set of variants, but when there is only one variant in the condition (e.g. --condition=1:1:C:T) I get this …
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Hello,
I encountered a bug/unexpected behavior with the SKAT results when only a single variant is kept for analysis.
Instead of results_SKAT$test.snp.mac returning me the single variant's name and…
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nucdiff formating of vcf variant files that are then "prepared" aka, fix the format, before annotation with vcf-annotator has "bugs"
This is fixed with prep_vcf_annotator.py
1. Adding info Colum…
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Hi Anni,
First many thanks for your contribution in AMR risk assessment. It's very useful.
Here I have two questions. The first one is about Rank-IV ARGs. From our metagenomics analysis we found tha…
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> Single variant meta-analysis fails with an error unless a set test option is listed in the command, but runs fine as long as one set test flag is included. However, the command as a whole still erro…
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Hi guys,
I get regular requests from collaborators to look if we have seen germline variants in a specific gene within our AFHCS or GA cohorts. I've created a 'Gene Search' analysis to have a quick…
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## Goal:
- What proportion of variants and which ones show a signal relative to their WT?
## Basic Analysis using mean profiles:
- Using correlation coefficients (by Marzieh)
- [x] Replica…
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For example, in [one instance in SQLite](https://sqlite.org/src/info?name=6166a30417b05c5b2f82e1f183f75faa2926ad60531c0b688a57dbc951441a20&ln=827-828), UTF characters are scanned by checking whether t…