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Old 01-07-2014, 06:58 AM   #1
Location: New York

Join Date: May 2010
Posts: 14
Default what is the meaning of vcf-stats output for shared snps??

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

Last edited by BGould; 01-07-2014 at 07:55 AM. Reason: answered
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snp analysis, snp filtering, vcf-stats, vcftools

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