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'''GLF''' is a format for storing marginal likelihoods for next-generation sequence data, conditional on a set of possible genotypes.
'''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 [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> command, which requires a sorted [[SAM]] file and a [[FASTA]] file with the human genome reference sequence.
GLF files can be generated using [http://samtools.sourceforge.net samtools]. To generate a GLF file, use the <code>samtools pileup -g</code> 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
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
== File Format ==
The GLF-file format is defined in an Appendix to the [http://samtools.sourceforge.net/SAM1.pdf SAM-file format specification].
The current specification (GLF version 3) follows. All integers in are stored in the little-endian byte order. Most GLF files are compressed in a GZIP compatible format; SAMTOOLS will only read GLF files that are compressed with the BGZF library.
=== Header ===
Each GLF file starts with a header that identifies the files.
char[4] magicNumber = "GLF\3"; // This identifies the file format
int32_t headerLength; // This is typically zero
char[headerLength] headerText; // This is typically unused
=== Chromosome Header ===
The main header is followed by a series of blocks, summarizing likelihoods along each chromosome. Each of these blocks starts with a header, that records the chromosome label and length.
int32_t labelLength; // Including the terminating null character
char[labelLength] label; // Printable string identified the chromosome label; typically, "1", "2", "3"... "22", "X", "Y", "MT" are used as labels for human chromosomes.
uint32_t chromosomeLength; // Length of the original reference sequence. This is a useful sanity check, but samtools can generate GLF entries that go past the end of the sequence.
=== Likelihood Record Header ===
Each chromosome header is followed by a series of likelihood records, terminating with an end record of type 0.
char refBase:4; // 0..15 => XACMGRSVTWYHKDBN, so that 0x01 = A, 0x02 = C, 0x04 = G, 0x08 = T
char recordType:4; // 0 for the last record in this chromosome, 1 for regular records, 2 for indels
=== Simple Likelihood Record ===
These are records with recordType = 1.
uint32_t offset; // Offset from the previous record
uint32_t:24 depth; // Depth of coverage for the current record
uint32_t:8 maxLLK; // Maximum log-likelihood, multiplied by -10 log 10
uint8 mappingQuality; // Root mean squared mapping quality
uint8_t llk[10]; // Log-likelihood for each genotype, in the order AA..AT..CC..CT..GG..TT
=== Indel Likelihood Record ===
These are records with recordType = 2.
uint32_t offset; // Offset from the previous record
uint32_t:24 depth; // Depth of coverage for the current record
uint32_t:8 maxLLK; // Maximum log-likelihood, multiplied by -10 log 10
uint8 mappingQuality; // Root mean squared mapping quality
uint8_t llkHomozygous11; // Log-likelihood for an allele 1 homozygote
uint8_t llkHomozygous22; // Log-likelihood for an allele 2 homozygote
uint8_t llkHomozygous12; // Log-likelihood for an allele 1/2 heterozygote
int16_t signedAllele1length; // Length of the first indel allele (positive=ins; negative=del; zero=no-indel)
int16_t signedAllele2length; // Length of the first indel allele (positive=ins; negative=del; zero=no-indel)
char indelSequence1[signedAllele1Length]; // Sequence of the first indel allele
char indelSequence2[signedAllele2Length]; // Sequence of the first indel allele
=== Last Record ===
These records are empty.
