this was answered . . .
One of the output files of vcf-stats tool, (*.shared), seems to indicate it counts only only sites where the samples of interest share a non-reference allele. Is this true?? If so, is there a way to find the TOTAL shared alleles (reference or non-reference allele) using this tool?
out.shared :
#Shared SNPs Frequency
0 1383802
1 574506
2 495679
One of the output files of vcf-stats tool, (*.shared), seems to indicate it counts only only sites where the samples of interest share a non-reference allele. Is this true?? If so, is there a way to find the TOTAL shared alleles (reference or non-reference allele) using this tool?
out.shared :
#Shared SNPs Frequency
0 1383802
1 574506
2 495679