Entering edit mode
5.9 years ago
M
•
0
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 :)
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