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a running error when running vcf-isec

1) shared SNPs in all three samples

$ vcf-isec -n +3 4751_97PASS.vcf.gz 4751_42PASS.vcf.gz 4751PASS.vcf.gz | gzip -c > 4751shared.vcf.gz &

2)Error

$ Leading or trailing space in attr_key-attr_value pairs is discouraged:
    [Description] [DP < 5 ]
    FILTER=<ID=LowCoverage,Description="DP < 5 ">
 at /hpf/tools/centos6/vcftools/0.1.14-6/share/perl5/Vcf.pm line 180

[1]+  Done                    vcf-isec -n +3 4751_97PASS.vcf.gz 4751_42PASS.vcf.gz 4751PASS.vcf.gz | gzip -c > 4751shared.vcf.gz
vcf-isec
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updated by Zev.Kronenberg Zev.Kronenberg • written by zengtony743 zengtony743

1 answer

The error is self explanatory. You have a space between the 5 and the ". it should be "DP < 5" >. Also it is isn't that smart to use '<' within a description field.

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written by Zev.Kronenberg Zev.Kronenberg

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