Integrative Genomics Viewer modified to work with the application programming interface of Intrepid Bioinformatics

<p>Integrative Genomics Viewer developed by the Broad Institute modified to work with the application programming interface of Intrepid Bioinformatics (http://server1.intrepidbio.com/).</p

Variant Call Format Records.

<p>An example of three variant call format records. The first is a called heterozygote with an allele depth of 11, 6 reads containing the reference allele, and 5 reads containing the non-reference. The second, a called homozygote in the current analysis with an allele depth of 4, three high quality reads containing the non-reference allele and one low quality read containing the reference. The third, is an example of a called homozygote with an allele depth of 5, where all 5 reads contained the non-reference allele. Images of the reads used to derive the VCF records are shown within the IGV Browser. Base calls within the reads that agree with the reference are not rendered.</p

DOI for the annotation data produced in this work.

<p>DOI for the annotation data produced in this work.</p

Called homozygous variants for which the reference was not detected in Twilight.

<p>Called homozygous variants for which the reference was not detected in Twilight.</p

Variation identified in mapped Twilight Illumina data set.

<p>Variation identified in mapped Twilight Illumina data set.</p

Variation identified in mapped Twilight Sanger data set.

<p>Variation identified in mapped Twilight Sanger data set.</p

Incorrect Base Assignments.

<p>An example of incorrect base assignments. A) Variants (indicated by the red shading) that are called homozygous (indicated by the turquois shading) differences measured by the UnifiedGenotyper in both the Illumina and Sanger datasets are shown here. In B), it is demonstrated that a single low quality Sanger read was used as the basis for the consensus sequence in this region. The UnifiedGenotyper, however, ignores this read due to the low phred quality scores in the region. The phred based quality scores are indicated for the 4 miscalled bases. The corresponding NCBI Trace Archive Trace Name and TI# are G836P5757RI23 and 1325049864 respectively, with bases 594–630 as the region of interest. This region may be viewed in IGV at <a href="http://dx.doi.org/10.13013/J6VD6WCM" target="_blank">http://dx.doi.org/10.13013/J6VD6WCM</a>. The link will download a JNLP file that webstarts IGV centered on region of interest. Bases within the reads that agree with the reference are not rendered.</p

Summary of mapping statistics for the Twilight Sanger reads.

<p>Summary of mapping statistics for the Twilight Sanger reads.</p

Depth of Sanger Read Coverage.

<p>A graph of depth of coverage for the mapped Sanger reads. The shaded gray box highlights the percentage of reads covered by one or two reads.</p

Twilight discrepancies resolved by Bravo data.

<p>An example of a region showing homozygous differences between Twilight and the reference which are resolved by alleles from Bravo. Region may be viewed in IGV at <a href="http://dx.doi.org/10.13013/J63X84K9" target="_blank">http://dx.doi.org/10.13013/J63X84K9</a>. Link will download a JNLP file that will webstart IGV, centered on region of interest. Bases within the reads that agree with the reference are not rendered.</p