Add a module to filter variants post-merge in bulk pipeline.
I've typically used the following:
vcftools --gzvcf ${MY_VCF} \
--max-missing 1.0 \ # may want to lower this
--min-alleles 2 \
--max-alleles 2 \
--remove-indels \
--out snps_filtered \
--recode --recode-INFO-all
We may also want to add a filter for common variants based on a reference. Historically this was done from genomics with --maf 0.05, but I believe this is calculated based on the dataset, so it would be highly sample-size dependent, and would not accomplish what we are hoping for.
Add a module to filter variants post-merge in bulk pipeline.
I've typically used the following:
We may also want to add a filter for common variants based on a reference. Historically this was done from genomics with
--maf 0.05
, but I believe this is calculated based on the dataset, so it would be highly sample-size dependent, and would not accomplish what we are hoping for.