Entering edit mode
6.3 years ago
vinayreddynannuru
▴
20
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