Open dfornika opened 3 years ago
Good catch - I guess the problem is that I run bcftools csq
on the unfiltered vcf (which already breaks calls downstream of a low-AF frameshift), then filter the broken calls for AF later - by this point the damage is already done.
I think I'd like to output the un-AF-filtered vcf somewhere, but as in https://github.com/BCCDC-PHL/type-variants-nf/pull/4/files, i'll add the AF filter to the vcf before calling bcftools csq
- does that seem like an OK solution?
That sounds good to me.
@dfornika It is my first time to use the pipeline and I tried to annotate using the -gff option but I got an error. I simply downloaded the reference.gff file from NCBI so not sure if this is the right file or there is something else that I need to use. It would be great if you can share the gff file that you use or guide me where I can find it. Thanks
@ahmedmagds look in the typing
directory of this repository
@dfornika Thank you!
Having the same issue with a low-frequency frameshift upstream of N501Y etc, which in turn are not called.
Good catch - I guess the problem is that I run
bcftools csq
on the unfiltered vcf (which already breaks calls downstream of a low-AF frameshift), then filter the broken calls for AF later - by this point the damage is already done.I think I'd like to output the un-AF-filtered vcf somewhere, but as in https://github.com/BCCDC-PHL/type-variants-nf/pull/4/files, i'll add the AF filter to the vcf before calling
bcftools csq
- does that seem like an OK solution?
Yeah, that would be great to have the original vcf file with all detected variants kept somewhere.
Running
type_vcf.py -dp 10 -af 0.75
on the following input:...results in the following
.csq.vcf
:Note the variant at position 22000:
...is included in the
.csq.vcf
file despite havingALT_FREQ
of0.409091
. This introduces a frameshift in theS
gene that interferes with consequence assignment downstream:resulting
SAMPLE.variants.csv
file is:...as a result, the
VOC-202012/01
variant is not called.Should variants be excluded from the
.csq.vcf
file if theirALT_FREQ
is below--allele_freq_threshold
? I've implemented that in another repo where I've extracted out the typing portion of this pipeline and it does recover the correct variant calling for this example.https://github.com/BCCDC-PHL/type-variants-nf/pull/4/files