Mike Lloyd

Fritz, It is HiFi reads. I am mapping to a draft genome, which has a number of small contigs. I am thinking this may be the cause. I am going...

any ETA on when the fix will be on CRAN?

I am trying this new feature, but I am hitting a problem when running `--un` with `--sam-append-comment`. When you specify to output unmapped reads to a new fastq, the resulting...

As an update, it could be a possible work around to have a FREEC specific input parameter, which would use a different FREEC formatted SNP file. I found a [perl...

@cyruinous did you ever work out a solution to the above issue you laid out?

Seeing the same issue, and your case you provided is a perfect summary. If you extend your command a bit, to include `annoDb="org.Mm.eg.db", flankDistance = 1000, addFlankGeneInfo = T` in...

Actually, this is a common issue here. See #2 and #12 and #31 and #109 and #113 and some explanation here: http://guangchuangyu.github.io/2014/10/multiple-annotation-in-chipseeker/

I observe the same issue with other SV types, and I would love to hear the answer. I emailed the developers, and never heard back. Perhaps someone will reply here.

I re-ran without `--score all` and the run completed without issue. Can you advise, is this a bug or did I enter the command incorrectly?

It does appear to be related to the lack of `SVLEN` in MantaINS calls. If you spoof a file that includes fake SVLEN values, the MantaINS calls will merge.