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I aim to detect a variant at chr5:51902807 in 1,700 bam files (It is a rare variant; AC
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Hi @heathsc
I'm using BSCall software to detect some variants from whole genome bisulfite sequencing data.
My version of bs_call is 2.1.7
When I tried to compare the result of BSCall and NA1…
tahuh updated
2 years ago
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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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Hey,
We only get a vcf file for tag genomes and SNP files for each genome in gt_results. Do you have any suggestions for making a SNP matrix of all genome?
Thanks!
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I'm trying to use VarDictJava 1.7.0 to call a duplication in some hybrid capture data. I'm attempting to establish a lower limit of detection both in the number of DUP-informative reads and the allel…
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2 VCFs with different blocking schemes
De novo calling:
- PASSing sites only
- Removed * allele and X chromosome
- Minimum PL = 20
- Minimum child Allele depth = 20%
Unfiltered calls s…
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A bug in the core pindel code is currently incorrectly calling complex indel regions. These calls have the same reference allele value and alternative allele value. They should not pass when using fla…
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Howdy all,
So running into an odd issue. I am running a few K. pneumoniae samples against an MLST database using 0.2.0, and on first run, it generated the following best match:
![image](https://…
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### Description of the bug
Dear All,
I launched the variant calling step using the ASCAT tool, but I received an error message that I did not understand. Could you please help me resolve this issu…
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`mlst-seeker cache` should update existing records when the PubMLST database updates. For records that have all assigned alleles but no ST, re-attempt assigning ST using new ST definitions. For record…