Weisheng Wu

Hi, I got an error message saying: > 2020/08/26 23:40:29 Running command: protein_alignment_from_nucleotides -v pan_genome_sequences/proS.fa > 2020/08/29 12:26:05 Running command: prank -d=pan_genome_sequences/proS.fa -o=pan_genome_sequences/proS.fa.aln -codon -F -quiet -once > /dev/null 2>&1...

How to merge indels

2

I'm calling variants from 10 samples using one reference fasta for all. The samples are from the same strain. One sample is WT and the others were under different stress...

Hi, Is there a way to find out fold-back inversions from the Manta calling results? Thanks,

Miscalling of HomRef?

1

I've run Manta on a WGS sample and one of the called variants was labelled as "HomRef" in the FT field in one sample: > chr1 2789490 MantaBND:0:14411:14412:0:7:0:0 T ]chr11:44096312]T...

1/0 genotype generated by "bcftools norm" at multi-allele sites

2

I ran "bcftools norm" to split multi-allele variants into individual rows. For some of them, 1/0 genotypes were generated. For example, this variant ``` 1 970549 . TGGGG TGG,TGGG,TG,T,GGGGG 1.53856e+06...

Velocyto quits without error

5

I tried to run velocyto run10x to generate loom from the outputs of a cellranger run. It successfully generated the cellsorted bam, but it quit during counting. I tried it...

If I run rectangle directly on my epiread it says: "**[main_rectangle:79] Error, rectangle cannot cross chromosomes**". The manual does not say the input has to be chromosome split. If I...

IndexError: list index out of range

4

My commdand-lines: ``` # NanoSim v3.1.0 singularity run -B /nfs/ nanosim_v3.1.0.sif read_analysis.py genome \ -i all.pass.filt.fastq \ -rg 741_wzi_types.fa \ -o training \ --chimeric \ -t 40 singularity run -B...

Support for Dorado?

1

Any plan to add `dorado` to `--basecaller`? Thanks.

Sniffles version: 2.2 (pulled from: `docker://quay.io/biocontainers/sniffles:2.2--pyhdfd78af_0`) Command-line: ``` sniffles \ --sample-id {wildcards.sample} \ --reference {params.ref} \ --input {input} \ --vcf {output} \ --no-qc \ -t {threads} \ --mosaic \ --minsvlen...