Question: **Is nonreference discordance just (Number of ALT mismatches/Number of ALT matches)*100?**
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gravatar for curious
8 months ago by
curious460
curious460 wrote:

Im looking at vcf-compare: http://vcftools.sourceforge.net/perl_module.html#vcf-compare

The docs say: The script also computes numbers such as nonreference discordance rates

when running 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?

vcf-compare vcf • 180 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by curious460
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