octopus

octopus copied to clipboard

Hello there, # Adding AVX support I just wanted to say thank you for creating this awesome tool. If it wouldn't be too much work, would it be possible to...

skchronicles

**Describe the bug** Segmentation faults occurs when running the Cell command **Version** ```shell $ octopus --version octopus version 0.7.4 (HEAD ed012a6) Target: x86_64 Linux 3.10.0-862.14.4.el7.x86_64 SIMD extension: SSE2 Compiler: GNU...

chenv3

Install fails on Apple M1

1

I am trying to build the docker image on a MacBook Pro with M1 Max Pro chip. I try using both `arm64` and `native` for the `--architecture` option. In either...

jdidion

How to install forest model with conda installed version?

1

**Describe the bug** A clear and concise description of what the bug is. I would like to install the forest model with the conda installed octopus. However, from ur documentation...

yangyxt

Segmentation fault when reference genome contains '.'

1

**Describe the bug** Thanks for the great tool! If the reference fasta contains one or more '.', instead of a nucleotide, it fails with a segfault. I successfully run `octopus`...

bricoletc

very slow call set refinement with refcall

1

The call set refinement step of octopus (v0.7.4 or development) when using the refcall option runs very slowly (50min with a 1.5Mb reference genome at 50X coverage). The initial calling...

nemartins

very low -B, safe? && core dump 'what(): BadRegionCompare:'

1

# A question and a Bug Report ## Is setting -B very low going to negatively impact var calling? - I ran a parameter space scan of -X and -B...

iamh2o

ERROE:Phred: negative error probability -0.000000

6

Hi! When I run the program using the following command： octopus -R /home/cluster/Storage3/LB_NA/hs37d5/hs37d5.fasta \ -I /home/cluster/Storage3/LB_NA/preprocess/normal.bqsr_realigned.bam /home/cluster/Storage3/LB_NA/preprocess/tumor.bqsr_realigned.bam \ -N normal --somatics-only --forest $forest --threads 32 -o /home/cluster/Users/lxy/octopus.vcf I met a...

xixi1998815

elongated runtimes for deep-sequencing data in cancer calling mode

3

Hi, I am trying to use octopus for liquid biopsy samples. In this context I have deep (10,000x) targeted (~1.3Mb Panel) sequencing data which are preprocessed by deduplication and bqsr...

iserf

somatic calling: inconsistent ploidy

5

**Describe the bug** Calls in the same phase set have different plodies. **Version** ```shell $ octopus --version octopus version 0.7.4 Target: x86_64 Linux 3.10.0-957.5.1.el7.x86_64 SIMD extension: AVX2 Compiler: GNU 10.3.0...

jbedo