When running GATK baserecalibrator on SOLiD read data, I initially obtained the following error:
ERROR MESSAGE: SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@7cc9970a is malformed. Please see http://gatkforums.broadinstitute.org/discussion/1317/collected-faqs-about-input-files-for-sequence-read-data-bam-cramfor more information. Error details: Unable to find color space information in SOLiD read. First observed at read with name = 872_727_11 Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.
I attempted to correct this (as advised by material on the GATK site) using the --solid_recal_mode flag, but upon implementation of BaseRecalibrator with this flag
java -Xmx16g -jar $gatkJar -nct 8 -allowPotentiallyMisencodedQuals -T BaseRecalibrator --solid_recal_mode SET_Q_ZERO -rf BadCigar -I $Pfx.realn.bam -R $hgReference -knownSites $dbsnp -o $Pfx.recal.grp --lowMemoryMode & >> $Pfx.step2.log
I obtain precisely the same error (i also attempted to run it with -solid_recal_mode REMOVE_REF_BIAS, with the same results). Is there something else that can be done about this space color error?