hello all,
has someone used HaloPlex data (agilent, similar SureSelect) for detection of very rare mutations (down to 0.5%)?
this means very deep data (up to few 100k coverage) for very small regions (~10 k bases). HiSeq 2500 150 PE.
suggestions? other callers for very rare SNVs?
thank you,
dietmar
has someone used HaloPlex data (agilent, similar SureSelect) for detection of very rare mutations (down to 0.5%)?
this means very deep data (up to few 100k coverage) for very small regions (~10 k bases). HiSeq 2500 150 PE.
Code:
my pipeline will look like this: - remove adaptors and low quality bases (Q10 or higher?) -(?) error correct (e.g. with ecc.sh (BBmap)) - BRIAN: do you think this is wise, or will i remove also rare SNVs (the data are up to few 100k's deep) - map to genome (BBmap) - realign INDELs and recalibrate quality (GATK) - call SNVs, using following callers: --- freebayes --- loFreq --- MuTect
thank you,
dietmar
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