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MLEAF and MLEAC

gilgigilgi Member
edited August 2012 in Ask the GATK team

Dear GATK team,

We were looking in the documentation for an explanation for MLEAC and MLEAF in the FORMAT column of the VCF file, but didn't find what it stands for. Can you help please?

Best Answer

  • delangeldelangel Broad Institute ✭✭
    Accepted Answer

    We'll be changing the phrasing of this description (and the name itself) in a future release to make it clearer. It's the ML number of alternate alleles for each individual sample at a site. It's equivalent to the sum of "1"'s in a genotype (for a biallelic site).

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    Hi there,

    Have you taken a look at the VCF header (where all of the INFO and FORMAT fields are defined) for your file? Incidentally, these are INFO fields not FORMAT fields.

  • gilgigilgi Member
    edited August 2012

    Yes, I looked there. These values appear both in the FORMAT and the INFO field:

    ##FORMAT=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed, for this pool">                                                                
    ##FORMAT=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed, for this pool">                                                               
    ##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">                                                             
    ##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">                                            
    

    If I understand it correctly, in the INFO - it relates to reads from all samples, and in the FORMAT- for each sample separately.

  • delangeldelangel Broad InstituteMember ✭✭
    Accepted Answer

    We'll be changing the phrasing of this description (and the name itself) in a future release to make it clearer. It's the ML number of alternate alleles for each individual sample at a site. It's equivalent to the sum of "1"'s in a genotype (for a biallelic site).

  • gilgigilgi Member

    Thanks a lot!

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