I used the following vcftools filter commands --geno and --hwe to filter VCF file
vcftools --vcf sample.vcf --hwe 0.001
vcftools --vcf sample.vcf --geno 0.9
Both created log files named out.log. But could not find the output file.
Like for example when we use vcftools --relatedness --vcf generates default output file named out.relatedness
However the log file (out.log) for --geno option has the following lines
File contains 259375 entries and 435 individuals. Applying Required Filters. Filtering sites by allele frequency and call rate After filtering, kept 435 out of 435 Individuals After filtering, kept 197076 out of a possible 259375 Sites Run Time = 41.00 seconds
Any help much appreciated
Thanks, Tinu
vcftools –vcf sample.vcf –hwe 0.001 --recode
Adding recode option will produce an output file named out.recode.vcf which will have filtered data.
Adam Auton helped by replying to the same question posted in VCFtools help discussions
To specify the suffix for the output file (instead of "out"), use the --out option
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