search

tgen / vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files
Other
5 stars 1 forks source link

vcfMerger could use Pisces module #21

Closed sfacista closed 2 years ago

sfacista commented 4 years ago

We are using http://uswest.ensembl.org/Canis_familiaris/Info/Index for a reference genome. Unfortunately, all we have left is normalized VCF. I have to go back in a re-run to generate raw VCF's. All I have left right now is the compressed/ normalized VCF's. I will attach it as soon as I acquire it.

ChristopheLegendre commented 4 years ago

@sfacista Hi Sal, What is the issue you are trying to describe? Could you be more specific regarding the error you got while running vcfMerger2 for canine?

PedalheadPHX commented 4 years ago

The request is to develop a prep script for PICES (https://github.com/Illumina/Pisces) vcf files, I ask Sal to provide some examples

ChristopheLegendre commented 4 years ago

Sorry for the confusion. I thought Pisces was the name of an organism; In latin, Pisces means "fish" or thought it could be related to canine ; I did not think about a toolname. :-)

Sure we can make a prep script and update the current vcfMerger2 with that tool.

ChristopheLegendre commented 2 years ago

'won't implement'

This won't be implemented as of today; If example of Pisces somatic VCFs are provided and Pisces appears to be an accurate and fast somatic variant caller after the submitter of the issue or anyone else has shown us comparisons with other callers, please feel free to re-open the issue. Thanks. Best. C.