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Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Request for clarification of code comment on type of alignment performed by Haplotypecaller (pairHMM) #5529

Closed sooheelee closed 5 years ago

sooheelee commented 5 years ago

Researcher reports a discrepancy in code comments (two occasions) vs. what is actually implemented in the code. The concern is that pairHMM actually performs global alignment (Durbin Figure 4.2) but the code comments indicate local alignment and Durbin Figure 4.3.

Hello, thank you for your reply. The algorithm is clear to me, from what I read of the code it is effectively the right of figure 4.1 (or 4.2 without the start and end states for simplicity) that is used and not 4.3

Therefore my concern, the comments in the source code clearly state that 4.3 is used and that it is local alignment, while the code in fact does global alignment.

It makes more sense to do global alignment (sequence to sequence, like Needleman-Wunsch) and this is what the codes seems to do (does).

Thank you for your answer.

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sooheelee commented 5 years ago

Can you please help clarify @ldgauthier or @davidbenjamin? Many thanks.

sooheelee commented 5 years ago

Looks like the researcher is one step ahead and filed a pull request at https://github.com/broadinstitute/gatk/pull/5528.

droazen commented 5 years ago

Closed by https://github.com/broadinstitute/gatk/pull/5528