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grch37-lite in Call Somatic Mutations WGS

aleehongaleehong BroadMember, Broadie

TARGET WGS data was aligned to GRCH37-lite. Internally, GP has aligned to Hg19. Is there a easy way to merge the two together without having to realign the TARGET data (and take up a lot of space realigning)?

I ask since I'm trying to use Call Somatic Mutations WGS in firehose but because GRCH37-lite is slightly simplified, there are contigs that are missing and thus the process fails.

Alternatively, are there annotations somewhere for the GRCH37-lite that I could use? I don't see it on Algorithms Commons.

Thanks,
Andy H.

(Sorry if this is an over simplification... I'm still pretty new to this)

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @aleehong
    Hi Andy,

    Unfortunately, there is no easy way to merge together read data that was aligned to two different references. Are you saying you are not able to call variants in Firehose with GRCH37-lite? If so, what kind of error do you get?

    You may be interested in Picard's LiftoverVCF. With that tool, you can take the variants from GRCH37-lite and match those sites to the ones from the hg19 reference.

    -Sheila

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