JoannaTan

Errors when run with large number of samples

7

Hi @brentp, I ran smoove v0.2.2 using singularity and I run it as part of a nextflow process. When I execute with small sample size (i.e. 30, 100, and 300),...

How does Minimac4 handle large chunks of missing genotype when creating reference panel

4

Hi, I am trying to impute my data using my own reference panel. However, my reference panel has many blocks of missing genotypes. I am wondering if minimac4 can handle...

ALT field only contains symbolic <INS>, <DEL>, ... tags instead of actual ALT nucleotide sequence

1

Hi Tobias In the issue https://github.com/dellytools/delly/issues/344 you mentioned that "for an insertion there should always be an ALT sequence". I am using Delly version 1.1.6 (admitely old given the current...

vcf_merge for SV

1

Hi @hannespetur, We ran graphtyper2 using v2.5.1 two years ago to re-genotype SVs. We noticed that vcf_merge in v2.5.1 does not include the --sv parameter. Can we still merge the...

Hi, We have ran multiple SV callers for short-read data and we want to merge the calls across SV callers and re-genotype our CRAM files using paragraph. Is there any...

Dear authors of Spectre, i ran the epi2me wf-human-variation workflow to process our ONT long read data to obtain the sniffles2 and spectre output. For the sniffles2, the wf-human-variation workflow...