Help With Custom Vcf-Annotate Feature In Vcftools

Question

[714]

Hi guys,

I am still trying to familiarise myself with perl and NGS-based bioinformatics tools. In the VCFtools' vcf-annotate feature, there is an option to customise your filtering. I have tried the following script (named filter.txt) to filter out those with a minimum QUAL score of 20:

#filter qual score 
 tag      => 'QUAL',
 name => 'phred score of wrong ALT call',
 desc=> 'phred score too low',
 apply_to => 'SNPs',
 test     => sub { if ($MATCH >=20) {return $PASS;} else {return $FAIL;}}

I then type the following command:

zcat AD0062-C.vcf.gz | vcf-annotate -f filter2.txt > out.txt

However this gives me the error "Can't use string ("tag") as a HASH ref while "strict refs" in use at /usr/bin/vcf-annotate line 172". I know that is giving me the warning that "tag" is not a hash element, however I'm not sure how to fix this.

Answer 1

[Alex Paciorkowski]

Can't you just do this as a one-liner in VCFtools? You can do filtering this way as well.

Try

zcat AD0062-C.vcf.gz | vcf-annotate -f Q>=20 > out.txt