Does the VCF file need to be filtered, such as minor allele frequency (MAF)?
I've found that this has a significant impact on the results.
My VCF file has only undergone hard filtering with GATK.
I attempted to add the -m parameter to filter the VCF.
Without filtering by MAF.
My command is: ./RAiSD -n Rus -I input.vcf -f -R -A 0.01 -S Rus.list.
After filtering out SNPs with a MAF of less than 0.05, the calculated μ values all approach zero.
My command is : ./RAiSD -n Rus -I input.vcf -m 0.05 -f -R -A 0.01 -S Rus.list.
Does the VCF file need to be filtered, such as minor allele frequency (MAF)?
I've found that this has a significant impact on the results.
My VCF file has only undergone hard filtering with GATK.
I attempted to add the -m parameter to filter the VCF.
Without filtering by MAF.
My command is: ./RAiSD -n Rus -I input.vcf -f -R -A 0.01 -S Rus.list.
After filtering out SNPs with a MAF of less than 0.05, the calculated μ values all approach zero.
My command is : ./RAiSD -n Rus -I input.vcf -m 0.05 -f -R -A 0.01 -S Rus.list.