Reference mismatch

[denisemauldin]

Hi there,

I was wondering if you'd consider implementing a specific flag for vt normalize. We're getting an error that looks like this with some of our genomes:

Variant is not consistent: chrY:59034049-59034049 - N(REF) vs A(FASTA)

This is because it's in the PAR region and the reference we're feeding it has that masked. We don't really want to use the -n flag because we would like to catch other errors if they happen, but we'd like to ignore errors where the REF is N.

Thanks,
Denise

[atks]

The -n flag when enabled, will still output the message that the reference is not consistent. Is it possible to make a scan of the logs for such warnings that do not occur in the the pseudoautosomal regions?

[denisemauldin]

Hi there,

It is possible to do that, but we have 7k+ genomes that we're processing, so having an additional process to scan the logs is additional overhead. Figured I'd inquire here whether it'd be possible to have a flag for ignoring this specific case.

Thanks,
Denise

[atks]

I'm a bit hesitant about having that additional feature as I'd prefer that errors are captured. It is definitely possible though but I need to convince myself that it is necessary.

Is it possible for the normalization step to use a reference sequence file which does not mask those bases. Because I assume that the variants were called using a reference that did not mask those bases in the first place.

[denisemauldin]

Hi there,

I do prefer that it prints the log, but that we can not have vt exit when it runs into a REF N situation. I'm inquiring about an additional flag. Example behaviour:

vt normalize -o output.vcf -r hg19.ref.fa input.vcf
-> dies on all reference mismatches
vt normalize -n -o output.vcf -r hg19.ref.fa input.vcf
-> warns on all reference mismatches
vt normalize -s -o output.vcf -r hg19.ref.fa input.vcf
-> warns on reference mismatches where ref is N, dies on other reference mismatches

Thanks,
Denise

[atks]

Ah, I understand now. I think that is a good feature.

[atks]

can you please pull it and try it. The option is -m

http://genome.sph.umich.edu/wiki/Vt#Normalization

[slagelwa]

FYI seems to be working well. Thanks.