tsimakova@biolinux:/opt/vcftools_0.1.12b/perl$ ./vcf-compare -c chr9 /home/tsimakova/examples/2055-3-1_v2.vcf.gz /home/tsimakova/examples/2055-3-2_v2.vcf.gz
# This file was generated by vcf-compare.
# The command line was: vcf-compare(r953) -c chr9 /home/tsimakova/examples/2055-3-1_v2.vcf.gz /home/tsimakova/examples/2055-3-2_v2.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      1       /home/tsimakova/examples/2055-3-1_v2.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
Warning: Read 0 lines from /home/tsimakova/examples/2055-3-2_v2.vcf.gz, the tabix index may be broken.