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Old 10-15-2013, 02:59 PM   #1
bruce01
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Default vcf-compare output

I am looking at some VCF files; I like the output from vcf-compare, eg:

#SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN Number of REF matches: 297982
SN Number of ALT matches: 262298
SN Number of REF mismatches: 4131
SN Number of ALT mismatches: 35684
SN Number of samples in GT comparison: 0

but now want to get the actual lines from my VCF that correspond to what is of interest (eg number of REF mismatches). I am intermediate at Perl and had a look at the script but it is WAY over my head! Can anyone give me any ideas on how to cajole the REF mismatches from my VCFs?
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