GATK IndelRealigner make mistakes

Question

[whaiyu06]

hello,

I used the command to realignment around indels.The command as follows:

java -jar /Software/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar \
-R $ref \
-T IndelRealigner \
-targetIntervals A01-2m-B8_merge.mark.intervals \
-I  A01-2m-B8_merge.mark.bam  \
-o  A01-2m-B8_merge.mark.realn.bam \
-known /dbsnp/Mills_and_1000G_gold_standard.indels.b37.vcfs \
-known /dbsnp/1000G_phase1.indels.b37.vcf 2>stderr/A01-2m-B8_merge.GATK_IndelRealigner.stderr

and met the error message:

SAM/BAM/CRAM file htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter@15f11bfb is malformed. Please see https://www.broadinstitute.org/gatk/guide/article?id=1317for more information. Error details: the BAM file has a read with no stored bases (i.e. it uses '*') which is not supported in the GATK; see the --filter_bases_not_stored argument. Offender: E00477:238:hggvjccxy:7:2217:26890:33762

What should I do ?Thanks very much

Answer 1

[Pierre Lindenbaum]

what is the output of

samtools view A01-2m-B8_merge.mark.bam | grep -F 'E00477:238:hggvjccxy:7:2217:26890:33762'

as stated by GATK , I suspect that it contains a 'NO-BASES/*' flag in the read sequence. GATK is not able to handle this.

[whaiyu06]

Thanks.There nothing output as your command.

[whaiyu06]

I solved this issue by adding another parameter -filterNoBases. Thanks for your advice.