imputation accuracy in beagle
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2.6 years ago

hello all,

i wanted to calculate the imputation accuracy for my data in beagle. there is an output below when i compared my unimputed vcffile with imputed file that contains only randomly selected positions. how much is the accuracy 100% or 99.1%

 This file was generated by vcf-compare.
 The command line was: vcf-compare(r953) ../vcffiles/gbs.africa.exclude.gz ../../imput.vcf.gz
VN 'Venn-Diagram Numbers'. Use `grep ^VN | cut -f 2-` to extract this part.
VN The columns are:
VN        1  .. number of sites unique to this particular combination of files
VN        2- .. combination of files and space-separated number, a fraction of sites in the file
VN  136     ../../imput.vcf.gz (100.0%)     ../vcffiles/gbs.africa.exclude.gz (0.9%)
VN  14843   ../vcffiles/gbs.africa.exclude.gz (99.1%)
SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN  Number of REF matches:  136
SN  Number of ALT matches:  136
SN  Number of REF mismatches:   0
SN  Number of ALT mismatches:   0
SN  Number of samples in GT comparison:    0

thanks,

vinay

beagle • 717 views
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