I want to compare two vcf file
common_and_clinical_20150106_bgzip.vcf.gz and variants_bgzip.vcf.gz
When I run on terminal
vcftools --gzvcf common_and_clinical_20150106_bgzip.vcf.gz --gzdiff variants_bgzip.vcf.gz --diff-indv-map --out output_file
the error is
Error: Unknown option: output_file
and when I run
vcftools --gzvcf common_and_clinical_20150106_bgzip.vcf.gz --gzdiff variants_bgzip.vcf.gz --diff-indv-map --out
the error is
Reading individual mapping file. Error:Could not open map file: --out
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written
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Anop Singh Ranawat •
vcftools --gzvcf common_and_clinical_20150106_bgzip.vcf.gz --gzdiff variants_bgzip.vcf.gz --diff-indv-map --out output_file
The --diff-indv-map expects a file.
From Manual:
--diff-indv-map <filename> This option allows the user to specify a mapping of individual IDs in the second file to those in the first file. The program expects the file to contain a tab-delimited line containing an individual's name in file one followed by that same individual's name in file two with one mapping per line.
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written
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GouthamAtla
hi Geek_y I know command --diff-indv-map but why error?
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written
by
Anop Singh Ranawat •
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