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Can VG simulate the third-generations long reads?

5

Hi. Now I have the `.gbz` graph file, and I want to simulate the third-generations `long reads` data from a pangenome graph. Can VG simulate the third-generations long reads? Or...

tanger-code

Merging multiple graph files

4

Hi! I have constructed the multiple graphs and i want to combine that to a single graph file. But I found that both `vg combine` and `vg ids` can combine...

Lucio-Yang

Error Exceeded Limit of Size on Disk While Running vg index

1

Description: While attempting to run the `vg index` command to generate GCSA index files from multiple `.vg` files, the process terminated due to a size limit being exceeded. The error...

AishaAlsuwaidi

Construct a generation-level pan-genome

5

In the future, I want to map the resequencing data of different species of onto my map genome.Then the group vcf with good classification is used to carry out the...

jwli-code

Mapping paired reads w/ giraffe, no EOF marker, job stalls, exit code 79

5

I am mapping paired end reads to HPRC-GrCH38 (indexed with vg autoindex) `vg autoindex --workflow giraffe -x grch38.xg -g grch38.gcsa -g /path/to/file/grch38/hprc-v1.0-minigraph-grch38.gfa -p GRCH38_pangenome --target-mem 80G -t 20 > grch38_pangenome.girrafe.gbz...

AlphaJulietAlpha

ERROR vg autoindex :Tag "transcript_id" not found in attributes (line 145). ERROR: Tag "transcript_id" not found in attributes (line 4). ERROR: No transcripts parsed (remember to set feature type "-y" in vg rna or "-f" in vg autoindex)

1

vg autoindex --threads 5 --workflow mpmap --prefix cattle --ref-fasta Cattle_ARS-UCD2.0_GCF_002263795.3_rename.fa --vcf cattle.variants.vcf --tx-gff cattlecattle.gff5 ：ERROR: Tag "transcript_id" not found in attributes (line 145). ERROR: Tag "transcript_id" not found in attributes...

08li20

Augmentation failed on one chromosome, but succesfull on other chromosomes

3

--> **1. What were you trying to do?** I tried to call vcf for each splitted chromosome after aligning short reads against the variation graph. **2. What did you want...

mas-agis

Genotyping SVs in a minigraph-cactus graph yields many similar alleles in output vcf

1

Hello, I have been trying to genotype structural variants from a graph made with minigraph-cactus, by mapping short reads with vg giraffe, then using vg pack and vg call to...

henrivkgt