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Pass `-known` to the IndelRealigner

Open smondet opened this issue 9 years ago • 3 comments

Add the option to be able to provide Mills_and_1000G_gold_standard.indels.vcf

smondet avatar Feb 16 '16 18:02 smondet

Does this restrict the set of indels that the IndelRealigner considers or expand it?

I don't really understand the Broad's explanation of this option: http://gatkforums.broadinstitute.org/gatk/discussion/4279/indelrealigner-known-resources

iskandr avatar Feb 16 '16 18:02 iskandr

Also, do they provide any VCF files for GRCh38?

iskandr avatar Feb 16 '16 18:02 iskandr

@iskandr I'm not sure, Brad Chapman has a thread on re-mapping and evaluating some of these resources on b38: https://github.com/chapmanb/bcbio-nextgen/issues/817

I haven't seen anything new that GATK explicitly supports b38, since the comment here: http://gatkforums.broadinstitute.org/gatk/discussion/3843/plans-to-update-the-gatk-bundle

The earlier Chapman thread also points to this for some discussion: https://www.reddit.com/r/genome/comments/3b3s3t/switch_from_hg19build37_to_hg20build38/

Looks like most of the being simply re-mapped to new coordinates

arahuja avatar Feb 16 '16 18:02 arahuja