GermlineEnrichment

Description

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

Caveats

• 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

Outputs

• BAM alignment
• VCF files
• QC metrics
• Tabix indexed coverage per base

Relatedness

• 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

Expected variant metrics

SNVs

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.

INDELs

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.

Source: http://gatkforums.broadinstitute.org/gatk/discussion/6308/evaluating-the-quality-of-a-variant-callset

Instructions

To resume pipeline from script 2

Delete all files in run folder except:

• Script 2
• Script 2 error and output log files
• Ped
• BAMs.list
• GVCFs.list
• HighCoverageBams.list
• Variables

From individual sample folders delete:

• runid_samplename_cnv.txt
• runid_samplename_cnv.vcf
• runid_samplename_cnv.vcf.gz
• runid_samplename_cnv.vcf.gz.tbi

Helper script: for i in $(ls */ -d); do echo $i; rm $i/*cnv*; done

Requeue script 2:

qsub 2_GermlineEnrichment.sh -v version=pipeline_version

e.g. for version 2.5.3 qsub 2_GermlineEnrichment.sh -v version=2.5.3