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Here is an example of how <code>glfTrio</code> works:
Here is an example of how <code>glfTrio</code> works:
lanecheck Input Files : --referencegenome [/usr/cluster/share/karma/NCBI36.fa], \
lanecheck --referencegenome /usr/cluster/share/karma/NCBI36.fa --dbSNPfile /home/1000G/data/GenomeSNP.dbsnp, \
--lanefile lane.lst --pedfile test.ped --datfile test.dat --mapfile test.map --prefix result
=== Input Files ===
=== Input Files ===
-f ''genotype likelihood file'' Father's [[GLF|GLF]]-format genotype likelihood file
lanecheck Input Files : --referencegenome [/usr/cluster/share/karma/NCBI36.fa], \
-m ''genotype likelihood file'' Mother's [[GLF|GLF]]-format genotype likelihood file
--dbSNPfile [/home/1000G/data/GenomeSNP.dbsnp], \
-c ''genotype likelihood file'' Child's [[GLF|GLF]]-format genotype likelihood file
--lanefile [], --pedfile [], --datfile [], --mapfile [], \
--mapquality [-1], --genocount [1000000], --nonrefhomo, \
--verbose, --coverage, --countbysite, --memorymap \
Output Files : --prefix []
--referencegenome ''genotype likelihood file''
--dbSNPfile ''genotype likelihood file''
--lanefile ''genotype likelihood file''
--pedfile
--datfile
--mapfile
=== Basic Output Options ===
=== Basic Output Options ===
lanecheck Input Files : --referencegenome [/usr/cluster/share/karma/NCBI36.fa], \
--dbSNPfile [/home/1000G/data/GenomeSNP.dbsnp], \
--lanefile [], --pedfile [], --datfile [], --mapfile [], \
--mapquality [-1], --genocount [1000000], --nonrefhomo, \
--verbose, --coverage, --countbysite, --memorymap \
Output Files : --prefix []
-b ''baseCallFile'' Specifies the name of the output [[VCF|VCF]]-format base call file
-p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''
-p ''threshold'' The threshold for base calling. Base calls will be made when their posterior likelihood exceeds ''threshold''
--reference Positions called as homozygous reference will be included in the output.
--reference Positions called as homozygous reference will be included in the output.
--minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.
--minMapQuality ''threshold'' Positions where the root-means squared mapping quality falls below this threshold will be excluded.
--strict When the map quality is interpreted ''strictly'', all three trio individuals must exceed ''minMapQuality''
--strict When the map quality is interpreted ''strictly'', all three trio individuals must exceed ''minMapQuality''
before a call is made. Without the --strict option, reads for individuals below the threshold are ignored.
--minTotalDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
--minTotalDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
