Question: redirecting vcftools file - tips
0
gravatar for muralinmars
4.5 years ago by
muralinmars70
France
muralinmars70 wrote:

Hi all,

 Here is the code that gets the VCF file from a specific region using `tabix` and then filters it for specific (european) population using 'keep' option from vcftools.

#select specific population
if [ "$POP_FILE" != "" ]; then
    vcftools --vcf temp.vcf --keep $POP_FILE --recode --recode-INFO-all > temp2.vcf 2> /dev/null
else
    cp -f temp.vcf temp2.vcf    
fi

PROBLEM: it creates the recode.vcf file but then the redirection is not happening as the temp2 file is empty

Any suggestions please,,,

linux vcftools sequencing • 950 views
ADD COMMENTlink written 4.5 years ago by muralinmars70
1
gravatar for Devon Ryan
4.5 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

Have you tried adding --stdout to the vcftools command?

ADD COMMENTlink written 4.5 years ago by Devon Ryan89k
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