baserecalibrator error: Unable to find color space information in SOLiD read
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8.0 years ago
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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 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?

gatk baserecalibrator • 2.0k views

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