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Old 03-02-2015, 10:19 AM   #3
clarissaboschi
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Location: US

Join Date: Apr 2010
Posts: 63
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Thanks sarvidsson

I saw this option. In my case I think the one that I need is:

#Only loci with enough reads supporting the variant will pass the filter
{
tag => 'INFO/DP4',
name => 'FewAlts',
desc => 'Too few reads supporting the variant',
apply_to => 'SNPs',
test => sub {
if ( !($MATCH =~ /^([^,]+),([^,]+),([^,]+),(.+)$/) )
{
error("Could not parse INFO/DP4: $CHROM:$POS [$MATCH]");
}
if ( 0.1*($1+$2) > $3+$4 ) { return $PASS; }
return $FAIL;
},
},

But I tried to edit this script to my need and did not worked... The way that the script is, is not what I want
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