Depth cutoff for heterozygyous missense SNVs?

smith-chem-wisc / Spritz

Software for RNA-Seq analysis to create sample-specific proteoform databases from RNA-Seq data

https://smith-chem-wisc.github.io/Spritz/

MIT License

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Closed acesnik closed 6 years ago

acesnik commented 6 years ago

Showed that depth cutoffs work to improve FDR for peptide identification in 10 cell lines paper
Apply cutoff to both alleles in heterozygous variations?
Heterozygous variation is included if any reads are found for the heterozygous allele, currently. This could be problematic. See https://github.com/acesnik/Bio.VCF/blob/master/VCF/GenotypeContext/Genotype.cs#L329.

acesnik commented 6 years ago

implemented this