Entering edit mode
3.9 years ago
switch.reem
▴
40
Hi all
How can I use impute2 to impute a VCF file filtering SNPs with low AF Like for example for the below record form a VCF file I would like to select only values with an AF value below 0.1 and use them for imputation. This is looking for rare values chr1 10333 rs1351390918 CT * 174.71 PASS AC=1;AF=0.004717;AN=212;BaseQRankSum=1.07;ClippingRankSum=0;DP=3933;ExcessHet=3.7566;FS=5.133;InbreedingCoeff=0.0853;MLEAC=7;MLEAF=0
Do I need to filter the vcf file first then use it for imputation or is there a parameter in impute2 that I can use to use on values with low AF?
