pioneer-pi

Now I want to get some information from pack file.

1

Now I use` vg pack` to get a packfile, They are read coverage in each base of variation graph. I want to get all the reads mapping to a special...

I have a question about x.snarls file.

16

I get a snarl file through` vg snarls *.xg > *.snarls`. What's the information of snarls file? I thought it was bubble of graph(it means between the start node and...

I have a question about vg's GAM file.

4

In GAM file, each line represent the result of one sequence map to variation graph. In it, there is a field called "from_length", a field called "to_length", What's meaning of...

I have a question while using vg.

6

Now If I want to execute vg's special format files like .vg,.snarls,.gam and so on. How can I read it directly to python with out transfer the special format to...

I use vg snarl to get the snarl fie of a variation graph. Can I get the reads which mapping to each snarl? Does vg support it?

When I use python bdsg to deal with a packedgraph, I found a question.

3

 1. I want to use follow_edges to get all the nodes which connect to node2, but i only get node3.(In fact, node3 and node4 are both its' connecting edges)....

In your example, I found [reading from stream](https://github.com/cartoonist/pystream-protobuf/wiki/Reading-from-a-stream) you import vg_pb2 to help parse GAM file, so what is it. If I want to use it, what do I need...

Hello, I have a question about vg map.

1

I check out the result(GAM file) of vg map. I found that there are some question in base repeat region. If there is a few bp deletion/insertion, the mapping information...

I use docker to start hap.py. The docker sentences: ``` docker run -it \ -v "${PWD}":"/input" \ -v "${PWD}/my_output:/output" \ jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \ /input/chr20.vcf.gz \ /output/my.vcf \ -f "/input/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_chr.bed" \...

Request for data and scripts for structural variant genotyping experiment

6

Dear VG team, I recently read your paper titled "Genotyping structural variants in pangenome graphs using the vg toolkit" , and I am very interested in reproducing the structural variant...