vcftools fst

Hi!

I'm trying to do a per-site Fst calculation with two populations. I'm running the following command lines :

VCF="/home/ndwivedi/work/structure_filter/scaffolds/${scaffold}.vcf.gz"

vcftools --gzvcf ${VCF} 
  --weir-fst-pop reunion.txt 
  --weir-fst-pop mauritius.txt 
  --out ./all_pops_${scaffold}

I keep getting the following error: Error: Unknown option: reunion.txt

My .txt files contain the names of the individuals as contained in the vcf (1 per line) which belong to each population.

For example: reunion.txt -->

1208_S43
1799_S40
2109_S41
2357_S36
2374_S37
2526_S35
261A_1_S38
263B_1_S39
503_S42
873_S10

Could you tell me why I get this error?

Thanks

fst vcftools

• 1,032 views • link

updated 3.6 years ago by Ram

• written 3.6 years ago by nishadwi •

1) retype the command from scratch to see if you inserted a weird character by mistake in the command line.

2) put echo before vcftools and show us the extact output.

• 0 views • link

written 3.6 years ago by Pierre Lindenbaum

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