Hello,
there is an error when I try to filter a VCF document for MAF. Here is a part of the the vcf-file:
2: chr1H 523 chr1H:523 C A . PASS . GT 0|0
1: chr1H 445 chr1H:445 C T . PASS . GT 0|
2: chr1H 523 chr1H:523 C A . PASS . GT 0|0
3: chr1H 535 chr1H:535 G A . PASS . GT 0|0
4: chr1H 587 chr1H:587 A G . PASS . GT 0|0
5: chr1H 757 chr1H:757 C A . PASS . GT 0|0
This is the command I’d like to execute:
~/vcftools_0.1.13/bin/vcftools --vcf prepared_chr_1.vcf --maf 0.05 --plink --out ~/input/strict.filtered.gwas.chr1
However, I get this error:
VCFtools – v0.1.13
(C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted:
–vcf prepared_chr_1.vcf
–maf 0.05
–out /proj/input/strict.filtered.gwas.chr1
–plink
After filtering, kept 1315 out of 1315 Individuals
Writing PLINK PED and MAP files …
Error: Could not open temporary file.
Do you have any suggestions? If I only use
~/vcftools_0.1.13/bin/vcftools --vcf prepared_chr_1.vcf --maf 0.05
without the –plink –out options, It seems to work but the output is of course not written into a file.
Thank you in advance for your answers!
Max
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