Molly Johnson

Deterministic Output?

10

Hi, I'm wondering if svaba is expected to have deterministic output, or if it's possible to get deterministic output? I've run svaba with the same settings on the same tumor-normal...

Calls Specific to High Coverage Data

1

Hi, We have been running multiple SV callers on high coverage data (275x tumor / 156x normal). We have observed that SvABA seems to be making quite a few SV...

Metadata ID Format

1

Hi, I've noticed that the paths to the bam files I'm using in my svaba runs are used as the sample IDs in the vcf files. I'm wondering if this...

DP=0, AD>0 and Incorrect Genotypes?

1

Hi Jeremiah, I've been seeing a few examples of somatic SVs where AD>0 and DP=0. I saw from issue [#29](https://github.com/walaj/svaba/issues/29) that AD can be greater than DP since discordant reads...

Hi, We previously used SnapATAC (v1.0.0) to run some analyses. We are hoping to wrap up those analyses using v1.0.0, but we need to re-install v1.0.0 and I can't seem...

I'm working on combining multiple mouse samples from two different sequencing runs (same tissue). I am combining the samples across sequencing runs as outlined in the tutorials into one snap...

seqnames in peaks / homer analysis

10

Hi, I'm trying to run Homer motif analysis on the peaks identified in my clusters, but it's giving an error because no knownResults.txt file is created. I've also noticed that...

CIGAR in sam file not showing mismatches

3

Hi, I'm looking at RNAseq data and am trying to identify the number of reads that map to an expressed transgene by using salmon in the quantification mapping mode. I...

Running SVTyper on any SV tool

8

Hi, I'm hoping to be able to run SVTyper in a generic mode on any SV tool. I have tried running SVTyper on Manta and SvAbA vcfs, and am running...