bkohrn

Lolipop with Mutant Allele Frequency instead of count

1

It would be useful if we could plot values other than count on the lollipop plot; in particular, we often find ourselves wanting to plot Mutant Allele Frequency. Ideally, this...

SeqLib::BamWriter.WriteRecord() seems to be truncating the qname field

2

When I create a new bam record, the new bam record seems to truncate the read name at 23 characters. I am using the following code (note that this is...

I've been using vcf2maf for a while, and just noticed while setting up a new computer that vcf2maf enforces the use of the ensembl-only vep cache (though this doesn't seem...

read_csv sometimes mis-identifies what type of column it should be reading and drops part of the column

1

I have a file that has a first column value of "8D": ``` ##Comments ##About ##File ##Creation #SAMPLE,REGION,MUTATION_TYPE,MUTATION_CLASS,COUNT,DENOMINATOR,FREQUENCY 8D,OVERALL,A>T,SNV,1,1000000,1.00e-06 8D,OVERALL,A>C,SNV,1,1000000,1.00e-06 8D,OVERALL,A>G,SNV,1,1000000,1.00e-06 8D,OVERALL,T>A,SNV,1,1000000,1.00e-06 8D,OVERALL,T>C,SNV,1,1000000,1.00e-06 8D,OVERALL,T>G,SNV,1,1000000,1.00e-06 8D,OVERALL,C>A,SNV,1,2000000,5.00e-07 8D,OVERALL,C>T,SNV,1,2000000,5.00e-07 8D,OVERALL,C>G,SNV,1,2000000,5.00e-07 8D,OVERALL,G>A,SNV,1,2000000,5.00e-07 8D,OVERALL,G>T,SNV,1,2000000,5.00e-07 8D,OVERALL,G>C,SNV,1,2000000,5.00e-07...

It would be nice to be able to use RefSeq or Merged caches (VEP options `--refseq` and `--merged`), instead of being forced into just using the Ensembl cache. So far...

GangSTR fails on small input files

3

I am part of a team doing targeted sequencing of PolyG loci. We have previously been using LobSTR for genotyping polyG sequences from reads prior to a consensus making step...

Allow multiple trim lengths or read structure in TrimFastq

6

It would be nice if we could either give multiple output read lengths (one per file) or a read structure (similar to what exists in FastqToBam) in TrimFastq.

lobSTR seems to mis-genotype reads (or at least some reads) where the STR (in this case, a poly-G region) has an N in the middle. Is there any way to...

I recently updated my R installation to R 4.4.1, and resetup all my packages, then went to do setup for a workshop that wanted me to install Azimuth. I got...

Error when using axis_logticks with pseudo_log transformation

1

I just updated to the latest versions of R and tidyverse (R 4.4.1, ggplot2 3.5.1), and decided to test out the new axis_logticks with a pseudo_log plot that I find...