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vg call report missing allele #4358
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I'm currently working to bring some of the recent
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Sure, please find the vcf at test.vcf.gz.txt. Below is the error message I got when using vcfbub:
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1. What were you trying to do?
Run
vg call
to genotype sample2. What did you want to happen?
Output a valid VCF
3. What actually happened?
The alternative allele is missing
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt
, please copy-paste the contents of that file here:NA
5. What data and command can the vg dev team use to make the problem happen?
I use the following command to call the SV from a haplotype sampled graph:
vg call -a -A -k $pack -S GRCh38 -t 40 -s HG00438 -O -z ${gbz}
The variant covered by another deletion has a "." in alternative allele. Does it mean "*" in VCF specification?
Besides,
vg deconstruct
will not output this variant when I use the command:vg deconstruct -P GRCh38 -a -t 40 -O $gbz
. In deconstruct's help, it says:Does it mean only in nested mode will output this kind of variants? Should
vg call
follow the similar behavior when not using-n
?One important issue with the missing alternative allele is that vcfbub cannot parse it:
Error when include the alt="." record:
No error when filter by "ALT!="."':
6. What does running
vg version
say?The text was updated successfully, but these errors were encountered: