how to call variance from vg multiple path alignment "mpmap" .gamp
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18 months ago
xwwang ▴ 20

Is there any instruction on how to call variance from vg's multiple path map output? I did not find information on how to call variance from multiple path map output.

details:

the multiple path map alignment output (.gamp) from mpmap and works well

Command:

vg mpmap -x $graph.xg -g $graph.gcsa -f sim.read1.fq -f sim.read2.fq -t 40 -m short > $graph.gamp

variance call:

I tried "vg pack" and then "vg call" for variance call. But is not working.
Command:

vg pack -x $graph.xg -g $graph.gamp -Q 5 -t 10 -o $graph.gamp.pack vg call -t 10 -m $mincov $graph.vg -k $graph.gamp.pack -s $samp -a >$graph.gamp.pack.vcf

error information:

[vg mpmap] elapsed time 11.6 m: Mapping finished. Mapped 3000000 read pairs. terminate called after throwing an instance of 'std::runtime_error' what(): obsolete, invalid, or corrupt protobuf input ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_c1eApl/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'std::runtime_error' what(): obsolete, invalid, or corrupt protobuf input ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_2ReQlP/stacktrace.txt Please include the stack trace file in your bug report! terminate called after throwing an instance of 'std::runtime_error' what(): obsolete, invalid, or corrupt protobuf input

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