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lanecheck --referencegenome /usr/cluster/share/karma/NCBI36.fa --dbSNPfile /home/1000G/data/GenomeSNP.dbsnp, \
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 ===
--referencegenome referencegenome file
--dbSNPfile dbsnp position file
--lanefile a list of lane file with path
--pedfile genotype information of the samples for checking
--datfile a companion data file for pedigree file (each row: M snpname, e.g. M rs1234)
--mapfile a companion data file for pedigree file (each row: chr snpname pos, e.g. 5 rs1234 56789)
--dbSNPfile ''genotype likelihood file''
--lanefile ''genotype likelihood file''
--pedfile
--datfile
--mapfile
=== Basic Output Options ===
=== Basic Output Options ===
--prefix specify the name of the output file
=== Filtering According to Depth and Map Quality ===
=== Filtering ===
--minmapquality reads with with mapquality falling below this threshold will be excluded
--strict When the map quality is interpreted ''strictly'', all three trio individuals must exceed ''minMapQuality''
--genocount the maximum number of genotypes compared
--verbose generate detailed
--coverage
--countbysite generate'' detailed statistic for each base compared
--maxTotalDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
=== Sample Labels ===
=== Other Options ===
--memorymap use memory map technique for efficient memory sharing
--child ''childLabel'' Specifies a label for the child, which will be included in the output VCF file
=== X Chromosome Variant Calling ===
=== X Chromosome Variant Calling ===
