I am new to GATK and have just run HaplotypeCaller several times according to the best practice. I am now planning to try Mutect2 to compare my normal and tumor samples, but am rather confused by the differences in the procedures between HaplotypeCaller and Mutect2. I have read several times on the GATK websites that "HaplotypeCaller and Mutect2 are quite different and employ distinct algorithms", but could not find answers to the questions below.
(1) Why doesn't HaplotypeCaller use PON, if PON is good to detect technical artifacts (especially when a single sample is analyzed by HaplotypeCaller)?
(2) Why doesn't Mutect2 have a VQSR step (or does it have)? Also, is it necessary to do BQSR before Mutect2 analyses?
(3) Why does HaplotypeCaller use 1000G and Hapmap etc (train and truth) while Mutect2 use gnomAD for germline resources (no vice versa)?
Thank you in advance.
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