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

Question

[idiaz026]

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

[glenn.hickey]

No, only GAM. See samtools stats for BAM stats.

You may also be able to convert your BAM to GAM with vg inject

Answer 1

[cfos4698]

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