Ryan Layer

Can you share what the two version, working and not working? On Thu, Dec 6, 2018 at 3:09 PM Alex Nesta wrote: > I ended up manually pointing to a...

Thanks! These are tricky issues that I cannot replicate so I want to get the info out there to help others out. On Thu, Dec 6, 2018 at 3:16 PM...

You can just not pass in the -sr argument. What is the mapping quality of that read? > On Jun 17, 2021, at 4:45 PM, Yiguan ***@***.***> wrote: > >...

> On Mar 11, 2020, at 2:52 AM, Limitto wrote: > >  > Dear, > > I used Lumpy via Smoove to call CNVs in a population of ~600...

If you are using smoove, then you shouldn't do those pre-processing steps yourself. Just run smoove call -x --name my-cohort --exclude $bed --fasta $fasta -p $threads --genotype /path/to/*.bam On Thu,...

I am not sure I understand the issues. DEL and DUP are CNVs.

We have never really tested anything but bwa aligned bams in a very long time. We did novoalign at first but dropped it once bwa mem came along. That is...

Ah. Yes. The bam filtering is much improved. Use smoove. We are ending support for lumpy express. > On Jun 18, 2020, at 12:39 AM, andrewSharo wrote: > > ...

You need to find the full set of SVs across all samples (typically called a sites vcf) then genotype all samples for this vcf with svtyper, then merge. smoove has...

Can you reach out to me personally so we can discuss? Ryan dot layer at Colorado > On Feb 19, 2021, at 5:20 AM, Camilo Chacon-Duque wrote: > > ...