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

Question

[Anop Singh Ranawat]

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

Answer 1

[GouthamAtla]

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.

[Anop Singh Ranawat]

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

[kautilya]

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