-
With #356, the VCF file created by `intrahost.py`'s `merge_to_vcf` reports read depth, at a given position, only for samples that contain alternate alleles at that position. If a sample has no alterna…
-
Project: 2520
Position: 284-285
Looks like there should be an A inserted between those two positions
/media/VD_Research/TMPDIR/2520_Projects/A12x2520_Houston_Mesoni
@InaMBerry
-
Hello
I have three questions pertaining to the VPhaser output
1) How do I interpret the output below ??
Pos Var Cons Strd_bias_pval Type Var_perc SNP_or_LP_Profile
1425…
-
I use Nextpolish on an HPC cluster, which is working flawless, if I use only short reads. But after activating the hybrid option (sgs+lgs), then it fails, delivering the following error massage. It is…
-
In preliminary testing, clumpify is much faster than mvicuna, but does not seem to remove as many reads with the settings I tried (subs=5 to match mvicuna and passes=4). On a bam file that mvicuna spe…
-
Hi,
I have noticed that kmc tool (latest release) generates wrong k-mers for long (>= 32) reads and short reads (~5) as well.
For example:
AACCACAGATATCTTTAACCAGGATACCATAGAC
the following sh…
-
The scaffolding stage does not always succeed for diverse genomes such as HIV or influenza.
The parameter space of the involved tools (currently `nucmer`, part of [`MUMmer`](http://mummer.sourceforge…
-
## Problem description
readjoiner fails with an assertion:
$ gt readjoiner overlap -readset samp -l 90
# gt readjoiner overlap (version 1.2)
# number of reads in filtered readset = 7960
Assert…
-
Apparently Illumina uses the Q=2 quality score as a "Read Segment Quality Control Indicator". I can't find any recent mentions of this on Illumina's website. One document from 2011 describes it as:
>…
-
Hello!
I just would like to know if technical support of Vphaser still works? If yes, where can I find it?
Sincerely,
Konstantin.