Colby Chiang

Including my response from the [other thread](https://github.com/hall-lab/svtyper/issues/10#issuecomment-412935721) here We don't have plans to add a quality filter to the SpeedSeq SV pipeline, but you can do it using awk: `cat...

Yes, try upgrading to pysam 0.8.1 or newer (https://github.com/hall-lab/svtyper/issues/37)

Yeah, the rationale behind this behavior is that we know that either PE or SR evidence may be blind to capturing the alternate allele at certain loci. This may be...

We've been using SVTyper on 30-50x human WGS with under 10 GB of memory (with no limit on --max_reads). However, we [exclude certain regions of the genome](https://github.com/hall-lab/speedseq#annotations) from LUMPY in...

I have no idea how svtyper will react to long-reads in general, but it looks like that problem is a result of improper read groups in your BAM. The easiest...

Ok, this may be a larger problem. Are you reads single end or paired end? SVTyper needs paired reads to calculate an insert size distribution

Right, that's an accurate description of the tool, but unfortunately SVTyper will not work for your data without modifications. It expects paired-end reads because it was designed for Illumina short...

Thanks for bringing this to our attention. It looks like some of the recent updates to LUMPY conflict with our Makefile. I've modified the LUMPY submodule in speedseq to resolve...

We've heard about this issue several times, but never with our own BAM files at WashU. Are you able to send a chunk of your BAM files that recreates this...

might be a duplicate of #40 . Is samtools in your PATH?