RUIXUE LIU
RUIXUE LIU
**1. What were you trying to do?** I'm tring to construct reference graph `bufo.vg` using reference `genomic.fna`, genome index `genomic.fna.fai` and vcf `bufo.12samples.vcf.gz`, vcf index `bufo.12samples.vcf.gz.csi`. I have to generate...
Research organism: bufo; Scaffolds of reference genome: 11 chromosomes and more than 700 unplaced contigs; Each sample bam file is split into three parts because sniffles run with error when...
Hello, I am dealing with 12 really big aligned bam files. So I had to divided them by 11 chromosomes, unplaced scaffolds and unmapped reads. So For one sample, there...
I use sniffles call variants on cluster. Firstly, I submitted sniffles jobs through slurm system. Every time it will be stuck at: ``` Info: xxx of xxx contigs in the...
python 3.7.9 sniffles 2.0.6 I run sniffles with **BAM+CSI** index on cluster. I don't know why the process is always stuck at ”building of index for XXX failed“. Here is...
Hi, I find two insertion records located in the same position when performing downstream analysis recently. There are 12 diploid samples in the VCF file. The ALT allele freq of...
I have a VCF file that consists of structural variant records. I'm trying to convert vcf to gds, but failed. The command I used is: seqVCF2GDS("/Users/path/12bufo.vcf.gz", "12bufo.gds", storage.option="ZIP_RA", parallel=8L) The...
**1. What were you trying to do?** run vg call to get vcf **2. What did you want to happen?** get all level variants, no matter top level or nested...
**1. What were you trying to do?** augment `sample1.gam` back to `graph.vg` **2. What did you want to happen?** generate augmented gam and vg files `sample1.aug.gam` `graph.aug.vg` successfully. **3. What...