kghimire

Accessing bwa mem inside docker.

1

Hi biodocker team,  I am building a fastq to vcf pipeline using bwa, gatk and picard tools. I implemented your code for docker image for bwa, gatk and picard. For...

Issue while running the executable.

5

Hi, I'm trying to use svtyper on my mac and after installation when I try to run the executable I get this error: % svtyper Traceback (most recent call last):...

Hi I Used this command: speedseq align \ > -o 5863-DD-3 \ > -R "@RG\tID:5863-DD-3\tSM:5863-DD-3\tLB:ILLUMINA" \ > assembly38.fasta \ > 5863-DD-3-R1_001.fastq.gz \ > 5863-DD-3-R2_001.fastq.gz I have the discordant and splitters...

Hi @ryanlayer, I have WGS 10x coverage paired-end fastq files and I want to call CNVs on these files. I aligned the files using bwa, and called lumpy traditional on...

Installation problem on mac Big sur

3

Hi, I have downloaded lumpy-sv from github. When I run the make command I am getting this error. checking for gcc... gcc checking whether the C compiler works... yes checking...