#29 Problem in interpretation of vcf-compare result
I have obtained following result after running vcf-compare
$ /home/priyanka/vcftools/src/perl/vcf-compare IRIS_313-10148.snp.vcf.gz CX120.snp.vcf.gz CX162.snp.vcf.gz
This file was generated by vcf-compare.
The command line was: vcf-compare(v0.1.14-12-gcdb80b8) IRIS_313-10148.snp.vcf.gz CX120.snp.vcf.gz CX162.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 625041 CX162.snp.vcf.gz (0.2%) IRIS_313-10148.snp.vcf.gz (0.2%)
VN 29727076 CX120.snp.vcf.gz (9.3%)
VN 34508665 CX162.snp.vcf.gz (10.6%)
VN 291435293 CX120.snp.vcf.gz (90.7%) CX162.snp.vcf.gz (89.2%)
VN 408832725 IRIS_313-10148.snp.vcf.gz (99.8%)
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: 108979 0.0% 409566745 409457766 IRIS_313-10148.snp.vcf.gz
SN Number of lost sites: 151042 0.0% 321313411 321162369 CX120.snp.vcf.gz
SN Number of lost sites: 229317 0.1% 326798316 326568999 CX162.snp.vcf.gz
But i am unable to interpret and plot the result. Please help me.
