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Badly formed genome loc ERROR

yotsusyotsus kyoto JAPANMember

Dear GATK help team,

I have a cut chromosome file (cur 17) in which I have processed through sorting, alignment, adding headers, and even through the realignertargetcreator. Yet, when I would like to call my indels from the Indel realigned. I have received an error.
ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The contig index 0 is bad, doesn't equal the contig index 17 of the contig from a string chr17

I have cut these chromosomes and processed the chr17 first since that is my region of interest, and did it since I thought it might save memory issues.

I am currently a newbie, have check the forum for help, yet only found one similar post with no solution.
Please help-- stuck at this stage. My code for the index realigned is the following:
java -jar /Users/yotsukurasohiya/build/softwares/GenomeAnalysisTK-3.2-2/GenomeAnalysisTK.jar -T IndelRealigner -R /Volumes/Pegasus/broadref/ucsc.hg19.fasta -I /Volumes/Pegasus/tmp/mardup.pregatk.bam -targetIntervals 2_target_intervals.list -known /Volumes/Pegasus/broadref/Mills_and_1000G_gold_standard.indels.hg19.vcf -known /Volumes/Pegasus/broadref/dbsnp_138.hg19.vcf -known /Volumes/Pegasus/broadref/1000G_phase1.snps.high_confidence.hg19.vcf -o 2_realigned_reads.bam

The heads that I have added are through picard softwares addorreplacereadgroups.
SO=coordinate CREATE_INDEX=true SM=temp PL=Illumina PU=barcode LB=bar ID=id

Best Answer


  • yotsusyotsus kyoto JAPANMember

    Thank you very much for your help! I have checked the FAQs for the -L augment. I have seen that is good for WES, which is my case. But I still cannot find an example of how to construct the argument? Can you please help me on that. I would like to specify particularly the 13th and 17th chromosome.

    Also, I saw in your previous thread that TCGA is the b37 build assembly, which I appreciate you bringing that up since I was aligning it with bwa with the hg19 build which may cause erroneous results.

    Thank you for your help in advance!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin



    If you want to specify the 13th and 17th chromosome, you can use:

    -L 13 -L 17

    You can also look here for an example:


    P.S. I will add a note to the FAQ article clarifying this.

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