Ryan Layer

No. It should be fine. > On Nov 6, 2020, at 6:51 AM, YiBenqiu wrote: > >  > Hello，I'm sorry to bother you. > I have some problems in...

To dig into this we will have to extract the problematic region of the BAM file. Please email me directly ryan dot layer at gmail to work out the particulars....

Can you check to see how big this file is /data/corpora/sge2/ lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_ 397.discordants.bam? On Tue, May 9, 2017 at 2:21 AM, amaiacc wrote: > Hi, > > I got the...

Do you think that you can send over these files: /data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam /tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib1.x4.histo /data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.discordants.bam /tmp/BILGIN_t0_397_k_SV_lumpy.vcf.sample1.lib2.x4.histo /data/corpora/sge2/lag/projects/lg-hand/working/Bordeaux/SV/lumpy/t0_397/t0_397.splitters.bam On Tue, Jun 6, 2017 at 11:52 AM, amaiacc wrote: > The file is 756M....

Merge first. I am not sure how bcftools merges SVs so you may want to look into that. That DP seems okay too. > On Jul 23, 2018, at 9:28...

SVTyper can take multiple bams, but I like to speed this process up by doing the genotyping of the two samples in parallel, then using bcftools to merge the two...

I am not sure. I have never tested this, but I would expect it to be okay. On Sun, May 17, 2020 at 3:06 PM icanwinwyz wrote: > Hello, >...

Yep. On Sun, Jul 12, 2020 at 7:37 PM Tianran YAO wrote: > @ryanlayer Do you mean that to be more > accurate one should merge two vcf files first...

Yes. DUP refers to a tandem duplication. On Wed, Jun 16, 2021 at 4:06 AM Jean-Baptiste Reynier < ***@***.***> wrote: > Hello, > > I had the same question: what...

Thanks for digging through and finding the bug! The latest wrapper for running lumpy, including merging multiple runs, is smoove https://github.com/brentp/smoove Please give it a try > On Jun 24,...