Changes

Here is an example of how <code>glfTrio</code> works:

Here is an example of how <code>glfTrio</code> works:

   lanecheck -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \

   lanecheck     Input Files : --referencegenome [/usr/cluster/share/karma/NCBI36.fa], \

        --father NA19239 --mother NA19238 --child NA19240 \

                  --dbSNPfile [/home/1000G/data/GenomeSNP.dbsnp],  \

        --minMapQuality 30 --minTotalDepth 0 --maxTotalDepth 1000 \

                  --lanefile [], --pedfile [], --datfile [], --mapfile [], \

        -b YRI.chrom20.SLX.vcf &gt; YRI.chrom20.SLX.log

                  --mapquality [-1], --genocount [1000000], --nonrefhomo, \

                  --verbose, --coverage, --countbysite, --memorymap \

  Output Files : --prefix []

== Command Line Options ==

== Command Line Options ==

=== Input Files ===

=== Input Files ===

  -f ''genotype likelihood file''    Father's [[GLF|GLF]]-format genotype likelihood file

-f ''genotype likelihood file''    Father's [[GLF|GLF]]-format genotype likelihood file

  -m ''genotype likelihood file''    Mother's [[GLF|GLF]]-format genotype likelihood file

  -m ''genotype likelihood file''    Mother's [[GLF|GLF]]-format genotype likelihood file

  -c ''genotype likelihood file''    Child's [[GLF|GLF]]-format genotype likelihood file

  -c ''genotype likelihood file''    Child's [[GLF|GLF]]-format genotype likelihood file

   --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.

                            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.

== '''TODO''' ==

== '''TODO''' ==

Frequently, we will want to run lane checking on a mapped .bam file which already contains sequence data from many different instrument runs merged together. They are merged because the sequencing center said they all belong to the same individual. In Pilot 3, this was true for all of the Baylor LS 454 sequencing data. In this case, the read identifier in column 1 of the .sam file carries information about which sequencing run each read belongs to, as well as information that uniquely identifies that read within its run. The read identifiers often are dot or colon-separated strings of the form 'run_name&lt;sep&gt;read_number'. The 'run_name' may be either an SRR / ERR identifier or the sequencing center's own alpha-numeric internal run identifier.

Frequently, we will want to run lane checking on a mapped .bam file which already contains sequence data from many different instrument runs merged together. They are merged because the sequencing center said they all belong to the same individual. In Pilot 3, this was true for all of the Baylor LS 454 sequencing data. In this case, the read identifier in column 1 of the .sam file carries information about which sequencing run each read belongs to, as well as information that uniquely identifies that read within its run. The read identifiers often are dot or colon-separated strings of the form 'run_name&lt;sep&gt;read_number'. The 'run_name' may be either an SRR / ERR identifier or the sequencing center's own alpha-numeric internal run identifier.

The "Read group classifier" is an extended regular expression such as '\(^[^.:]+\)[.:].*' which matches just the part of each read identifier that is common to all reads from one instrument run and which differs between instrument runs. The regular expression is passed into the lane checking program as an ascii string. The program keeps track of all distinct values it has seen for the matched portion, and must keep a separate tally of matches and mismatches for each combination of [read group x candidate individual]. By itself, the matched portion of each read identifier does not fully specify which original .fastq file a read came from. The 'bitwise flag' value in column 2 of the .sam format has the remaining information. This is able to distinguish between the 'left end', 'right end' and 'single end' reads which come from each Illumina paired-end sequencing run. The Baylor LS 454 data were all single end reads, so I did not have to deal with this complication.<br>

The "Read group classifier" is an extended regular expression such as '\(^[^.:]+\)[.:].*' which matches just the part of each read identifier that is common to all reads from one instrument run and which differs between instrument runs. The regular expression is passed into the lane checking program as an ascii string. The program keeps track of all distinct values it has seen for the matched portion, and must keep a separate tally of matches and mismatches for each combination of [read group x candidate individual]. By itself, the matched portion of each read identifier does not fully specify which original .fastq file a read came from. The 'bitwise flag' value in column 2 of the .sam format has the remaining information. This is able to distinguish between the 'left end', 'right end' and 'single end' reads which come from each Illumina paired-end sequencing run. The Baylor LS 454 data were all single end reads, so I did not have to deal with this complication.<br>