This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
The Splitting of BAM file (RNA-seq) before calling variants is throwing error
First of all I thank for the Tool , I am using this GATK var calling for my RNA-seq data.. I have been following the commands said in the site but its stopping me at the splitting BAM file step with the following error,
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR MESSAGE: Badly formed genome loc: Contig * given as location, but this contig isn't present in the Fasta sequence dictionary
The command I used is,
/opt/husar/bin/java-1.7 -jar /GenomeAnalysisTK-3.2-2.jar -T SplitNCigarReads -R /human_genome37_gatk.fa -I BM_ID_reorder.bam -o BM_ID_split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
I tried do variant calling on the duplicate removed BAM file, which also throwed error message as,
ERROR MESSAGE: SAM/BAM file BM_ID_reorder.bam is malformed: Reference index 1912602624 not found in sequence dictionary.
The command line I used for this,
/opt/husar/bin/java-1.7 -jar -Xincgc -Xmx1586M $NGSUTILDIR/java/GenomeAnalysisTK-3.2-2.jar -T HaplotypeCaller -R /human_genome37_gatk.fa -I BM_ID_reorder.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 -o BM_ID.vcf