vcf-compare venn diagram
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Entering edit mode
6.3 years ago

Hi!

I try to make a venn diagram with this command

vcf-compare -c 2.vcf.gz 4.vcf.gz 10.vcf.gz > venn.out

my question is...get this syntax error many times, is that normal? or I dont need to take care about it?

sh: 1: Syntax error: Unterminated quoted string
sh: 1: Syntax error: Unterminated quoted string
sh: 1: Syntax error: Unterminated quoted string
sh: 1: Syntax error: Unterminated quoted string
sh: 1: Syntax error: Unterminated quoted string
sh: 1: Syntax error: ")" unexpected
sh: 1: Syntax error: Unterminated quoted string
#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  53333   4.vcf.gz (100.0%)
#SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN  Number of REF matches:  53317
SN  Number of ALT matches:  53310
SN  Number of REF mismatches:   16
SN  Number of ALT mismatches:   7
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:   23  0.0%    53356   53333   4.vcf.gz`

Thanks!!

venn • 2.1k views
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