GATK BaseRecalibrator error message

[lre1234]

Hi all,
I am trying to run the BaseRecalibrator in GATK but got an error message of:

MESSAGE: SAM/BAM file SAMFileReader{test.sorted.bam} is malformed: The input .bam file contains reads with no platform information. First observed at read with name = 552_2035_733_F

I am assuming that this is telling me that I need the platform information to be contained in the read group (SOLiD sequencing in this case). I was under the impression that it is not necessary to have this information in the file, or am I mistaken by this? Should having this information really matter? Or am I missing some flag that should be added that will skip this.
Thanks

[vdauwera]

Platform information is indeed required by GATK.

Since you're working with SOLiD data, be sure to have a look at the solid-specific arguments of the BaseRecalibrator.

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html

[rpauly]

Hi,

I am getting the same error:
ERROR MESSAGE: SAM/BAM file SAMFileReader{*.bam} is malformed: The input .bam file contains reads with no platform information. First observed at read with name = HWI-ST565:24119R1ACXX:1:2106:16117:83155

This is illumina. How can I circumvent this error?

~Thanks!

[vdauwera]

You'll need to add the platform information to your read groups. You can use Picard tools' AddOrReplaceReadGroups (http://picard.sourceforge.net/comman...laceReadGroups) to reset the read group info.

[amitbik]

Hi All

I am getting error in BaseRecalibrator step. I am using this command

java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R file.fa -I file_relgn.bam -knownSites snv.sorted.vcf -knownSites indels_sort.vcf -o file_recal.grp -plots file_recal.grp.pdf

I am getting error like this

##### ERROR MESSAGE: Argument with name 'plots' isn't defined.

Any help will be appreciated.
Thanks in advance

[bruce01]

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_BaseRecalibrator.html

There doesn't seem to be an option to produce a plot from BaseRecalibrator. What are you trying to plot?

[amitbik]

I am trying to plot the graph before and after the baserecalibration.
here is the doc

https://www.broadinstitute.org/gatk//events/2038/GATKwh0-BP-3-Base_recalibration.pdf

[bruce01]

The 'empirical - reported quality' plots e.g. page 5? In the recal.grp file the data is available for this (RecalTable2, cols 2, 6) it should be trivial to plot in R.

[Zaag]

Hi All

I am getting error in BaseRecalibrator step. I am using this command

java -Xmx8g -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R file.fa -I file_relgn.bam -knownSites snv.sorted.vcf -knownSites indels_sort.vcf -o file_recal.grp -plots file_recal.grp.pdf

I am getting error like this

##### ERROR MESSAGE: Argument with name 'plots' isn't defined.

Any help will be appreciated.
Thanks in advance

It's a "new" tool.

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_bqsr_AnalyzeCovariates.html

[amitbik]

Thanks a lot bruce01 and Zaag

I think there is some problem in Rscript thats why it is showing error.
I did as mentioned in the link

http://www.broadinstitute.org/gatk/g...ovariates.html

But again i am getting error

##### ERROR MESSAGE: RScript exited with 1.

[Zaag]

Do you have ggplot2 (Rlibrary)?