Tumor normal variant detection
Tumor normal variant detection relies on the same method as somatic variant detection (Somatic variant detection), but has additional steps where variants that are assesed to be significantly present in the normal reads are removed.
Variant types
LightSpeed Fastq to Somatic Variants Tumor Normal reports reports SNVs, MNVs, InDels and replacements, provided that the variants are contained within at least one paired end read.
Variant annotations
Variants identified by LightSpeed Fastq to Somatic Variants Tumor Normal are annotated with the following basic information: Chromosome, Region, Type, Reference, Allele, Reference allele, Length, Zygosity, Count, Coverage, Frequency, Forward read count, Reverse read count, Forward read coverage, Reverse read coverage, Forward/reverse balance and Genotype.
Read more about these general variant annotations here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Variant_tracks.html.
In addition, variants called by LightSpeed Fastq to Somatic Variants Tumor Normal are annotated with both the same information as variants called by LightSpeed Fastq to Somatic Variants (Somatic variant detection) and information specific to the tumor normal analysis:
- Count in normal The allele count in the normal read mapping.
- Coverage in normal The coverage in the normal read mapping.
- Frequency in normal The allele frequency in the normal read mapping.
- p-value - global error rate in normal p-value from binomial test given normal count, normal coverage and an error rate of 0.005. Note that if UMIs are utilized, i.e., in the UMI step a UMI preset has been selected or a custom read structure with UMIs has been specified (see LightSpeed Fastq to Somatic Variants Tumor Normal), an error rate of 0.004 is used.
- p-value - global error rate in normal (phred-scale) Log transformed p-value - global error rate in normal.