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From: Ian D. <Ian...@ma...> - 2011-06-06 15:05:46
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Please can someone explain what the -Q flag in 'vcfutils.pl varFilter'. The only definition i can find is: Usage: vcfutils.pl varFilter [options] Options: -Q INT minimum RMS mapping quality for SNPs [10] Does it corresponds to a Phred score? Does it refer to the quality of a particular consensus base call or the SNP quality its (whatever that means)? I would like to be able to filter SNPs using the mpileup pipeline and it looks as the -Q option might help? Is this the same as (similar to) the 'samtools.pl varFilter' step used with pileup? E.g.: samtools.pl varFilter raw.pileup | awk '$6>=20' > final.pileup Many thanks! Ian PS i asked question in Biostars this morning if anyone wants the points. But non-one has answered yet. [http://biostar.stackexchange.com/questions/8873/meaning-of-samtools-vcfutils-pl-varfilter-q] |