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Old 03-08-2012, 05:10 AM   #1
Rubal7
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Location: Europe

Join Date: Jan 2012
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Default vcf-tools vcf-stats sample question

Hi all,

A quick vcf tools question. I am having problems with the -s option to only use listed samples with the vcf-stats tool. When I try the following:

vcf-stats -s Agg50 Agg51 Agg52 Agg53 Agg54 Agg55 Agg56 Agg57 Agg59 -f QUAL=10:200 /mnt/VCFFiles/Aggs.vcf -p /mnt/VCFFiles/Aggsstats

I get the error:

Unknown parameter or nonexistent file: "Agg51". Run -h for help.
at /usr/local64/bin/vcf-stats line 21
main::error('Unknown parameter or nonexistent file: "Agg51". Run -h fo...') called at /usr/local64/bin/vcf-stats line 65

Does anyone know what the problem is, I have tried using a file with the sample list too and it doesn't work.

Thanks,

Rubal7
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Old 04-09-2012, 01:42 AM   #2
AllanLindh
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Default Parameter order

I suspect you have long since figured this out, but while your command line agrees with the order show in the doc, all the examples have the vcf file before the options. Is it also possible that vcf-stats is one of the commands that actually requires the vcf files be compressed
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