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Old 05-08-2012, 01:01 PM   #1
Location: brussels

Join Date: Mar 2012
Posts: 13
Default gatk countcovariate ERROR MESSAGE Read starting with deletion. Cigar: 1D22M1I71M8S


I received targeted sequence reads from a 454 machine.
In my way on the application of the GATKV3.0 best practice guideline, I got the following error:

##### ERROR MESSAGE: SAM/BAM file SAMFileReader{/tmp/ISDBM229314/ISDBM229314.marked.realigned.fixed.bam} is malformed: Read starting with deletion. Cigar: 1D22M1I71M8S

I am using bwa0.6.1 hg19 and GATK1.6.2

Here is the pipeline:
1/ alignment using bwa bwasw -->sam
2/ use PICARD AddOrReplaceReadGroups to get an indexed BAM file:
java -Xmx4g -jar picard-tools-1.62/AddOrReplaceReadGroups.jar RGID=IDa RGLB=LB RGPL=454 RGPU=pu RGSM=sample SO=coordinate INPUT=sample.sam OUTPUT=sample.bam VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true
3/ GATK MarkDuplicates
4/ GATK RealignerTargetCreator
5/ GATK IndelRealigner
6/ PICARD FixMateInformation
7/ GATk CountCovariates --> ERROR MESSAGE
java -Xmx4g -jar GATK.jar -l INFO -R h37.fasta -nt 16 -knownSites:dbsnp,VCF dbsnp_135.b37.vcf -I sample.marked.realigned.fixed.bam -T CountCovariates --read_filter BadCigar -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile sample.recal_data.csv
I have the error with or without the option --read_filter BadCigar

any ideas? hints? links?
thank you for your help.
aituka is offline   Reply With Quote
Old 07-31-2012, 12:40 PM   #2
Junior Member
Location: USA

Join Date: Jul 2012
Posts: 1
Default Did you find solution

Hi aituka,

I have the sme problem. Were you able to find a solution? If yes, could you share?

newbie16 is offline   Reply With Quote
Old 09-13-2012, 06:07 AM   #3
Senior Member
Location: Budapest

Join Date: Mar 2010
Posts: 329

Our solution is simple: remove the read.
TiborNagy is offline   Reply With Quote

cigar, countcovariate, gatk, samfilereader

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