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Hi! In the vcf generated by NanoCaller there are some records that differ from others because they are only defined by ORP (Original variant position), ORL (Original reference length) and GQ (Genotype…
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Indels-2.0 is somewhat buggy at present. On several tests it simply fails. For example the test data from https://github.com/samtools/bcftools/issues/2277.
```
bcftools: bam2bcf_iaux.c:468: iaux…
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I am interested in the colibactin motif to see whether a mutation is likely be related to colibactin. In the original article, there was a clear notice of what an single base substitution colibactin-m…
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Hi there,
I am downloaded input files according to the documentation here: https://gagneurlab-drop.readthedocs.io/en/latest/prepare.html#files-to-download
For the high-quality variants, I can s…
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Hey I recently am running modkit on/around some structural variant calls. I was interested in using `modkit extract` to extract the methylation status within each reads on and around SVs. However, wh…
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when I run somaticseq "--run-mutect2 --run-vardict --run-lofreq --run-scalpel --run-strelka2 --run-somaticseq --run-workflow ", I found some indels had frequency of zero. For example,
chr1 1568…
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### Description of the bug
Hi, I’ve just run crisprseq using the targeted pipeline with a read1.fastq.gz only. I heavily quality filtered the input reads, removing any reads containing N characters.…
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```
Hello Rob,
I was just wondering if there is a way to include indels in the analysis.
Many thanks,
- Laurent
```
Original issue reported on code.google.com by `vtlaur...@hotmail.com` on 13 Dec 20…
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### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N c…
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With #754 we're halfway to also supporting inframe indels so we should just do the rest of the work necessary to support those types of proximal variants.