Entering edit mode

14 months ago

idiaz026
▴
10

Can vg stats -a be used on a bam file?

Can vg stats -a be used on a bam file?

0

Entering edit mode

14 months ago

idiaz026
▴
10

Can vg stats -a be used on a bam file?

0

Entering edit mode

14 months ago

cfos4698
★
1.1k

It requires graph format, not BAM:

```
$ ./vg stats
usage: ./vg stats [options] [<graph file>]
options:
-z, --size size of graph
-N, --node-count number of nodes in graph
-E, --edge-count number of edges in graph
-l, --length length of sequences in graph
-L, --self-loops number of self-loops
-s, --subgraphs describe subgraphs of graph
-H, --heads list the head nodes of the graph
-T, --tails list the tail nodes of the graph
-e, --nondeterm list the nondeterministic edge sets
-c, --components print the strongly connected components of the graph
-A, --is-acyclic print if the graph is acyclic or not
-n, --node ID consider node with the given id
-d, --to-head show distance to head for each provided node
-t, --to-tail show distance to head for each provided node
-a, --alignments FILE compute stats for reads aligned to the graph
-r, --node-id-range X:Y where X and Y are the smallest and largest node id in the graph, respectively
-o, --overlap PATH for each overlapping path mapping in the graph write a table:
PATH, other_path, rank1, rank2
multiple allowed; limit comparison to those provided
-O, --overlap-all print overlap table for the cartesian product of paths
-R, --snarls print statistics for each snarl
-F, --format graph format from {VG-Protobuf, PackedGraph, HashGraph, XG}. Can't detect Protobuf if graph read from stdin
-D, --degree-dist print degree distribution of the graph.
-b, --dist-snarls FILE print the sizes and depths of the snarls in a given distance index.
-p, --threads N number of threads to use [all available]
-v, --verbose output longer reports
```

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No, only GAM. See

`samtools stats`

for BAM stats.You may also be able to convert your BAM to GAM with

`vg inject`