Question: extract specific population (vcf) from 1000 genomes - keep option
0
gravatar for muralinmars
5.9 years ago by
muralinmars80
France
muralinmars80 wrote:

hi all,

how can i extract 1000 genome data in vcf format of a specific population using vcftools. Currently I am using tabix to download the data

tabix -fh ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr`echo ${REGION} | awk -F [\:] '{print $1}'`.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz $REGION > temp.vcf

and then include only the individuals from european population (CEU,GBR,FIN,TSI); through (--keep) option by providing a txt file (pop_file) including their individualIDs,,,

vcftools --vcf temp.vcf --keep $POP_FILE --recode > temp.vcf

where am i going wrong - As i producing the initial Vcf file but not after the filtering for specific pop.

Any suggestions PLEEEEASE

linux vcftools sequencing • 5.5k views
ADD COMMENTlink modified 5.9 years ago by Pierre Lindenbaum129k • written 5.9 years ago by muralinmars80
2
gravatar for Pierre Lindenbaum
5.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

when using

 

vcftools --vcf temp.vcf --keep $POP_FILE --recode > temp.vcf

 

the file temp.vcf will be overwittern before vcftools is started.

You're working with an empty file

 

Use

vcftools --vcf temp.vcf --keep $POP_FILE --recode > temp2.vcf

 

ADD COMMENTlink written 5.9 years ago by Pierre Lindenbaum129k

thanks... I tried to change the name of the VCF file (to temp2) generated after `keep` option,,,,

But it does not create the temp2 file (while the recode.vcf file is generated properly after filtering for specific population)

here is the code again

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

ADD REPLYlink written 5.9 years ago by muralinmars80

you're redirecting stderr to /dev/null what was the content of the error message ?

ADD REPLYlink written 5.9 years ago by Pierre Lindenbaum129k
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