Ben Weisburd

My environment is Groovy Version: 2.3.7 JVM: 1.7.0_71 Vendor: Oracle Corporation OS: Mac OS X When I try to run bpipe tests, I get "VerifyError: Bad method call from inside...

add ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz and CNV data to exac_browser.tar.gz related to #293

this is related to #282 once chrom, pos columns are removed, this will allow sorting by position.

these are redundant with the 'Variant' column

reference .bed files should have 0-based start coordinate

2

The [reference .bed files](https://github.com/gymreklab/GangSTR#gangstr-reference-files) currently use a 1-based start coordinate, but should be 0-based according to the .bed spec. Converting these to 0-based and re-running GangSTR significantly changes the output...

It's easy to create an OutriderDataSet with a countData matrix which has its columns in a different order than rows in the colData table. However, this leads to incorrectly assigned...

DownsampleSam discards NM tag

1

### Affected tool(s) or class(es) gatk DownsampleSam ### Affected version(s) GATK v4.3.0.0 ### Description Input cram file (gs://broad-public-datasets/CHM1_CHM13_WGS2/CHM1_CHM13_WGS2.cram) has NM tags, but the downsampled output file no longer has them....

Questions about optimal q and implementation="AE" vs. "PCA"

4

I understand using different values of q can significantly affect results, so I wanted to ask whether I'm choosing q and the `implementation` arg correctly. My dataset is 54 affected...

"Please provide hgnc symbols to compute gene p values!" error

1

I'm trying to run the latest version of FRASER. Everything works until I get to the results(..) function. The following code ``` library(FRASER) library(annotables) library(data.table) library(ggplot2) library(ggpubr) library(dplyr) library(purrr) library(ggrepel)...