"Error:Could not open map file: --out" in vcftools
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6.9 years ago

i want to compre 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

then 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

then error is

Reading individual mapping file. Error:Could not open map file: --out

 

next-gen SNP sequencing • 3.4k views
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Entering edit mode
6.9 years ago
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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6.8 years ago

hi Geek_y i know command --diff-indv-map but why error ??

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vcftools expects a mapping file after --diff-indv-map. As you are not specifying a filename and directly writing --out it is looking for a file named --out

If you have a mapping file then specify its name after --diff-indv-map

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