More posts like this
-
Can germline callers detect somatic variants? (RNAseq, cancer, no matched normal)
written by don •
-
Gatk haplotyper
written by prs •
-
Python for pdf reports
written by prs •
-
Extract somatic mutations and germline mutations from variant calling files?
written by ginnyli056 •
-
identifying TP53 germline mutations which are also in tumor cells.
written by lait
-
calling SV (or CNV) on CANCER SAMPLES with no GERMLINE
written by Bogdan
-
Strategies to call variants from a cancer sample
written by John Ma
-
CNVkit calling strategies with matched-normal tumor
written by fbrundu
-
Somatic and Germline variant calling in ion torrent
written by inayat45shaikh •
-
Identify Germline Mutations
written by yliuboston •
You need ClinVar, SIFT and PolyPhen2 annotations.
Use MuTect2 with the option
--genotype-germline-sitesto call variants. If necessary, use--genotype-pon-sitesas well.And I think I should add a step to filter out the common polymorphism before proceeding to find the pathogenic variants. Also, is there any database which has listed pathogenic variants for different cancer type?
Look at COSMIC - that's also a good source to annotate with. ClinVar is good for germline. Post gnomAD annotation, I use gnomAD non-cancer allele frequencies to filter variants.
So, if I am developing a pipeline only to find pathogenic germline variants, this is how I should start --> while variant calling, I can give known variant sites from dbSNP/gnomAD -->VCF --> removing common polymorphic site from VCF (using gnomAD non cancer alleles) --> Annotation of remaining variants using clinvar. Please let me know if this is a good approach or if I need to improve at any step.
I'd retain those sites and just add a flag. That way, you can filter them later if you need to. The pipeline looks fine otherwise.
Okay, thanks!