Addition of Y chromosome to the ref sequence

Question

[micro32uvas]

Hello,

I have aligned my WGS samples to a the latest bovine reference(B.tau5.0), available at NCBI. It is just yesterday, that in a pipeline used by 1000bull genome project, they have used the same reference merging the Y chromosome in it (B.taur5.0Y).

Now, I am not sure about it. Should I align all of my samples again? It would take huge time and resources. Is there any way to compensate and add the Y chromsome alignment that could save the current bams?

Any help is greatly appreciated.

I used bwa-0.7.17 and bwa mem for the alignment.

Ainnie

Answer 1

[Pierre Lindenbaum]

Should I align all of my samples again?

yes, adding new contigs removes false positives (think of a read matching 100% with 'Y' -> no variant, but matching with mismatches on chromosome '1' -> variant)

[micro32uvas]

What I dont get, is that the providers of the ref seq, (NCBI and Bovine database) have not given any newer version for the said purpose (The latest came by April 2018, and its done by PacBio). Now one of the pipelines, shared by the 1000 Bull genome Project, includes the Ref Seq (NCBI's Ref seq+ Y) and its provided at their site.

If the main providers have not updated a new/ modified reference, should I be even following the 1000Bull genome project's pipeline? Its more of a nightmare to start over, but is it worth the confidence?