output in VCF format - Githubissues

aryarm / varCA

Use an ensemble of variant callers to call variants from ATAC-seq data

MIT License

23 stars 7 forks source link

output in VCF format #6

Closed aryarm closed 4 years ago

aryarm commented 4 years ago

Add an option to the classify pipeline that would allow it to output predictions in the VCF format

aryarm commented 4 years ago

Strategy:

have a rank-ordered list of the callers in terms of the user's preference for using them
for each site, grab the REF/ALT alleles from the first preferred caller that supports the varca prediction
write that to a VCF file

Also recalibrate QUAL scores for the new VCF.

aryarm commented 4 years ago

To validate the VCF, I can try GATK's ValidateVariants and VCFtools' vcf-validator.

Update: The VCFs seem to pass GATK's ValidateVariants, as long as we fix the header with GATK's UpdateVCFSequenceDictionary or bcftools's reheader first.