kevlar

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Is kevlar able to detect duplications/repeat expansions and in general CNV?

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ashenflower

Kevlar novel multithreading

2

Hello, I launched kevlar as such ``` kevlar novel --out output.augfastq --case ../H5A3.cleanup.reads.fa --control ../ARC_ancestor.cleanup.reads.fa -t 48 --max-fpr 1.2 -M 10G ``` It has been running for 10 hours now....

ghost

> 30,000 variants reported from trio-analysis with FPR 0.001?

6

I'm seeing a very high number of reported variants from `kevlar`. Even after restricting the `max_fpr` values to `0.001` I'm seeing `> 30,000` variants? ## `config.json` ``` { "ksize": 31,...

moldach

count_control error: estimated false positive rate is 0.385 (FPR too high, bailing out!!!

5

After running successfully through the example dataset I've ran `kevlar` on my own data but am getting an error at the `count_control` step, that the FPR is too high. I'm...

moldach

VCF Parsing Issue

1

I'm running some BCFTools operations on the VCF outputs of the Kevlar pipeline (from simlike). It's a small issue, but the VCF syntax stumbles on the INFO lines: > ##INFO=...

17tranap

kevlar memory error

2

While trying the kevlar tutorial workflow, at kevlar partition step some files fail with memory error, I used 64g and 64g swap memory. ``` [kevlar::partition] Building read graph in relaxed...

sph17

Clarification - how to avoid high FPR

3

I'm trying to run Kevlar on a human trio, sequenced on a BGI-Seq 500, so the data has a fairly low error rate, but the reads are not error-corrected. For...

exeter-matthew-wakeling

Empty files produced by kevlar split cause crash of kevlar assemble

3

I am trying to run the [tutorial workflow](https://kevlar.readthedocs.io/en/latest/tutorial.html) with kevlar v0.7+15.gebabd62. The Snakemake workflow stops when coming to the rule "assemble", throwing the following error message: ``` Traceback (most recent...

serosko

It should be fairly straightforward to scan a final callset, identify any cases where multiple PASSing calls are derived from the same contig, and produce pileup images to facilitate manual...

standage

Report kevlar version when running a script

3

...for reproducibility's sake, yo.

standage