Im looking at
The docs say:
The script also computes numbers such as nonreference discordance rates
vcf-compare vcf1 vcf2 > out.txt
I get output that looks something like this:
# This file was generated by vcf-compare. # The command line was: vcf-compare(v0.1.14-12-gcdb80b8) snp.vcf.gz snp.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 281003 snp.vcf.gz (100.0%) #SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. SN Number of REF matches: 0 SN Number of ALT matches: 0 SN Number of REF mismatches: 0 SN Number of ALT mismatches: 0 SN Number of samples in GT comparison: 0 # Number of sites lost due to grouping (e.g. duplicate sites): lost, %lost, read, reported, file SN Number of lost sites: 341 0.1% 281344 281003 snp.vcf.gz SN Number of lost sites: 341 0.1% 281344 281003 snp.vcf.gz
Is nonreference discordance just (Number of ALT mismatches/Number of ALT matches)*100?