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  • vcftools flags --mac and --max-mac give empty output

    Hi everyone!
    I'm a newbie in NGS data analysis, that’s why I’m asking for some help in things that might be easy in fact.
    I have a zipped vcf –file, which contains human chromosome 20 sequences for 269 individuals. I want to filter out singletons and doubletons for subsequent analysis. I use vcftools v0.1.15 installed on a server.
    Here is what I do:

    Code:
    vcftools --gzvcf chr20_269ind.vcf.gz --mac 1 --max-mac 1 --recode --stdout | gzip -c > output_test.vcf.gz
    however, I get an empty output file (only sample names, no sequence information) and an error message that says as following:

    Outputting VCF file...
    After filtering, kept 0 out of a possible 991704 Sites
    No data left for analysis!
    Run Time = 24.00 seconds

    I’ve tried to play around with –-mac and –-max-mac flags. First I run the following line:

    Code:
    vcftools --gzvcf chr20_269ind.vcf.gz - -max-mac n --recode --stdout | gzip -c > output_tesmaxnt.vcf.gz
    where I tried n = 1; 10; 100
    All three attempts gave me the same output file (not empty this time) and the log file says:

    Outputting VCF file...
    After filtering, kept 991704 out of a possible 991704 Sites
    Run Time = 95.00 seconds

    Actually I get the same output if I run

    Code:
    vcftools --gzvcf chr20_269ind.vcf.gz --recode --stdout | gzip -c > output_tesmaxnt.vcf.gz
    Then I’ve tried running

    Code:
    vcftools --gzvcf chr20_269ind.vcf.gz --mac 1--recode --stdout | gzip -c > output_test.vcf.gz
    and got an empty output again
    Then I’ve run

    Code:
    vcftools --gzvcf chr20_269ind.vcf.gz --mac 0--recode --stdout | gzip -c > output_test.vcf.gz
    And got the same file as in case of --max-mac n
    It seems to me that these flags ‘see’ my file as if it contained only zeros, which is not the case (I’ve looked at the content of the file manually)
    If I try to filter for minor allele frequency instead of allele counts (which is not what I want to do, but I was just playing around to better understand what’s going on) I get this:

    Outputting VCF file...
    Error: Require Genotypes in variant file to filter by frequency and/or call rate
    I’ve tried vcftools versions 0.1.13 as well with no difference.

    Any help is greatly appreciated.

    Best,

    Vasili

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