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I'm trying to use GATK release2.0 with my nine exome-seq samples, following the steps on best practice I generated per-sample, ready-to-process .bam files and then used -T ReduceReads to generate .reduced.bam files for the next step (-T UnifiedGenotyper). When using these .reduced.bam files as UG input I receive this error message: "##### ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Too many deletions?" if I take my original .bam files as input things work smoothly. Do you have any idea what causes the problem?
Thanks a lot, Samira
Here is the command lines I use:
java -Xmx4g -jar $GATKv4 \ -R $GATK_BUNDLE/ucsc.hg19.fasta \ -T ReduceReads \ -L $capture_library.bed \ -I $i.recal_s.bam \ -o $i.reduced.bam java -jar $GATKv4 \ -T HaplotypeCaller \ -R $GATK_BUNDLE/ucsc.hg19.fasta \ -I InputReducedBams.list \ -L $capture_library.bed \ --dbsnp GATK_BUNDLE/dbsnp_135.hg19.vcf \ -o raw.snp.indel.UnifiedGenotyper.rsv.vcf