GLF

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GLF is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.

Generating GLF Files

GLF files can be generated using samtools. To generate a GLF file, use the samtools pileup -g command, which requires a sorted SAM file and a FASTA file with the human genome reference sequence. 

  samtools pileup -g -f human_b36_male.fa.gz NA19240.chrom21.SLX.maq.SRP000032.2009_07.bam > NA19240.chrom21.SLX.maq.SRP000032.2009_07.glf
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