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RevertSam in picards

I need to re-map two kinds of BAMS: a) the re-calibrated BAMs and b) hg19 mapped BAMs to hg38.

I am looking into the GATK tutorial: https://software.broadinstitute.org/gatk/guide/topic?name=tutorials#optionB, on "Convert aligned BAM to uBAM and discard problematic records using RevertSam", and below is an example.
java -Xmx8G -jar /path/picard.jar RevertSam \
I=6484_snippet.bam \
O=6484_snippet_revertsam.bam \
SANITIZE=true \
MAX_DISCARD_FRACTION=0.005 \ #informational; does not affect processing
ATTRIBUTE_TO_CLEAR=XT \
ATTRIBUTE_TO_CLEAR=XN \
ATTRIBUTE_TO_CLEAR=AS \ #Picard release of 9/2015 clears AS by default
ATTRIBUTE_TO_CLEAR=OC \
ATTRIBUTE_TO_CLEAR=OP \
SORT_ORDER=queryname \ #default
RESTORE_ORIGINAL_QUALITIES=true \ #default
REMOVE_DUPLICATE_INFORMATION=true \ #default
REMOVE_ALIGNMENT_INFORMATION=true #default

I have few questions:

1) The re-calibrated BAMs are generated using different GATK versions (3.4-3.6). What version of picard should we use for RevertSam?

2) Can we also use RevertSam on the mapped BAMs? If so, what parameters should be used?

3) It would be much appreciated if you can give more information on the parameters for this RevertSam:
a) MAX_DISCARD_FRACTION=0.005 --> if we don't want to discard any reads, we should set this value to zero, right?
b) What's your recommendation on ATTRIBUTE_TO_CLEAR? It's not clear to me how this parameter will work on top of REMOVE_ALIGNMENT_INFORMATION.

Thanks!

Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @yyee
    Hi,

    1) You should use the latest version of Picard for the best results. Have a look at this article for mixing and matching GATK versions.

    2) Have a look at this article.

    3a) Yes, if you don't want to discard any reads, you will need to set the parameter to 0.00. Please note, you may not be able to complete the run due to errors if you set the value so low. Have a look at the article from number 2 for more information.

    3b) I think the article from 2 will answer your question. Basically, those are tags not related to alignment information that you wish to clear.

    -Sheila

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