Benjamin Schuster-Boeckler

I think there are two confusions here 😅 I should not have mixed up two issues. One is that there seems to be a bug in the parsing of `0`s...

Hi guys, The fact that Canvas just consumes all the cores on the machine makes it extremely difficult to use in a shared resource environment like our HPC cluster. Also,...

I'm seemingly getting the same issue with the latest git master of bedtools and a vcf file generated with bcftools mpileup 1.9. I've attached the file here. The error I...

Ah! It's the weird way in which `bcftools` encodes the symbolic allele. The `` causes the error message. Maybe something to fix though, since most raw bcftools output includes these...

From a discussion at https://www.biostars.org/p/279971, I see that there is a reference to the newer VCF spec, which states: >.5 Representing unspecified alleles and REF-only blocks (gVCF) > > In...

As a recent twitter emigree, I concur with @ogrisel - I see a lot of _very_ long threads, especially by scientists and journalists who, for better or worse, use a...

Long-ish threads have become very common among many science Tweeters and journalists, and this is now washing over to Mastodon. There's a certain immediacy in having a longer discussion of...

Incidentally, I just got the same thing yesterday, and it's definitely Delly output. In the "sample1_sv.bcf" file, I have a line ``` chr1 40556015 DEL00000344 T 979 PASS IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv1.1.6;END=40562907;PE=18;MAPQ=60;CT=3to5;CIPOS=-73,73;CIEND=-73,73 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV...