I have computed the SNP annotation using snpEff using this following command line:
java -jar /apps/x86_64/snpeff/snpEff/snpEff.jar aa_stecla ./vcf/stec_stec_pool.filter.vcf > stec_stec_pool.filter_ann.vcf.
This generates an annotation file stec_stec_pool.filter_ann.vcf and a statistic summary file snpEff_summary.html. One of the table of the summary statistic file shows the number of LOW, HIGH and MODERATE impact variants as follow:
However, when I grep the those strings from my annotation file, I get different results:
grep -c HIGH stec_stec_pool.filter_ann.vcf
129
grep -c LOW stec_stec_pool.filter_ann.vcf
22930
grep -c MODERATE stec_stec_pool.filter_ann.vcf
10355
Do you have any idea why my numbers from 'grep' are lower than what I see in my in my summary file? which one to report?