Subsetting donor VCF file for Vireo strategy 2

[lucygarner]

Hi,

For strategy 2, you recommend subsetting the donor VCF file as below. Specifically how would you recommend to filter out SNPs with "too much missing values" or "genotypes too similar across donors"?

For efficient loading of donor VCF file, we recommend subset it bcftools view donor.vcf.gz -R cellSNP.cells.vcf.gz -Oz -o sub.vcf.gz

You can also add -s or -S for subsetting samples.

Make sure you only keep informative SNPs, e.g., by filtering out SNPs with too much missing values or the genotypes too similar across donors.

Best wishes,
Lucy

[huangyh09]

Hi, good question. You may try filtering out SNPs with missing values in >50% of donors or SNPs with the same genotype in >90% of donors. But this is just a rule of thumb and we haven't benchmarked on it.

Yuanhua

[lucygarner]

Thanks, and what software would you recommend to do this?

[ghuls]

@lucygarner You can use bcftools view for that.

Some examples:
https://github.com/aertslab/popscle_helper_tools/blob/master/filter_vcf_file_for_popscle.sh