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VCFtools pop_missing_filter.sh not working

Please help- I've come to use pop_missing_filter.sh script in VCFtools:

./pop_missing_filter.sh DP3g95maf05.recode.vcf popmap_VCF.tsv

But I get the following error message: 

Parameters as interpreted:
        --vcf DP3g95maf05.recode.vcf
        --keep CLAVP.keep
        --out CLAVP
        --missing-site

Keeping individuals in 'keep' list
After filtering, kept 0 out of 24 Individuals
Error: Require Genotypes in VCF file in order to output Missingness Statistics.
mawk: cannot open CLAVP.lmiss (No such file or directory)

This is the same for all my samples...

Cheers :)

assembly snp vcf
• 1,374 views • link
updated by Biostar Biostar • written by M • M

Hello M,

could you please describe what pop_missing_filter.sh should do? I couldn't found any documentation.

Also please post the header of your vcf file and the first 10 variant lines.

Use the code button (the one with 101010) to format the vcf content. I modified your post to display it correctly.

fin swimmer

• 1 views • link
written by finswimmer finswimmer

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