Diagnostic NGS pipeline for SNPs/Indels/CNVs/SVs/LOH from germline panel/exome data (Illumina paired-end)
Requires variables files. See https://github.com/mcgml/MakeVariableFiles
Launch with qsub 1_GermlineEnrichment.sh in the sample directory. Assumes Torque/PBS is installed
- BQSR requires at least 100M bases post filtering to create an accurate model. Roughly, it shouldn't be used for designs less than 0.5Mb.
- Script 2 requires PED file. By default, one is created assuming all unrelated samples. Downstream filtering assumes samples are unrelated unless specified in the PED
- BAM alignment
- VCF files
- QC metrics
- Tabix indexed coverage per base
- Not suitable for panel analysis
Same sample | 1st degree | 2nd degree | 3rd degree | Unrelated |
~0.5 | ~0.25 | ~0.125 | ~0.0625 | 0-0.04 |
Type | Variants | TiTv |
WGS | ~4.4M | 2.0-2.1 |
WES | ~41k | 3.0-3.3 |
If your TiTv Ratio is too low, your callset likely has more false positives.
Indel frequency | Insertion to deletion ratio |
Common | ~1 |
Rare | 0.2-0.5 |
A significant deviation from the expected ratios listed in the table above could indicate a bias resulting from artifactual variants.