GATK

Tagged with #index file
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Empty .idx file from unified genotyper

Hello,

I've been using GATK for a while now and suddenly when i run the unified genotyper (GATK version 1.5.21) my .vcf.idx files are empty. So the index file is produced but without any content.

This is how i run the command:

java -Xmx8g -jar $GATK_HOME/GenomeAnalysisTK.jar \
    -T UnifiedGenotyper\ 
    -I $SAMPLE\.sort-dup-realign-fixed-gatkrecal.bam\ 
    -R $REFERENCE\ 
    -o $SAMPLE\.raw.vcf\ 
    --annotation QualByDepth\ 
    --annotation HaplotypeScore\ 
    --annotation MappingQualityRankSumTest\ 
    --annotation ReadPosRankSumTest\ 
    --annotation FisherStrand\ 
    --annotation RMSMappingQuality\ 
    --annotation DepthOfCoverage\ 
    --genotype_likelihoods_model BOTH\ 
    -baq CALCULATE_AS_NECESSARY\ 
    --standard_min_confidence_threshold_for_calling 50.0\
     --standard_min_confidence_threshold_for_emitting 10.0\ 
     --min_base_quality_score 20\ 
    -l INFO\ 
    --dbsnp $DBSNP\ 
    -metrics $SAMPLE\.metrics\ 
    -L $TARGET_INTERVALS

Any ideas?

Regards,

Måns

IndelRealigner input file

Hello, I am a first-time user of GATK and have spent some time now on trying to get the input bam files in the appropriate format. To run IndelRealigner, I have added ReadGroups, Reordered and Index my bam file with the respective Picard-Tools.

My command-line is the following:

java -Djava.io.tmpdir='pwd'/tmp -jar GenomeAnalysisTK.jar -I ./add_read_groups_reorder_index.bam -R ./genome.fa -T IndelRealigner -targetIntervals ./gatk.intervals -o ./*.bam -known ./Mills-1000G-indels.vcf --consensusDeterminationModel KNOWNS_ONLY -LOD 0.4

I get the following message:

SAM/BAM file /home/gp53/tophat2-merge-ctl-1st-2nd-readgroups-reorder-index.bam is malformed: SAM file doesn't have any read groups defined in the header.

My reads are paired-end aligned with TopHat2 I will appreciate your help on this. Thanks, G.

Override index type/location on per file basis

Hi I'm getting an error "An index is required, but none found" for files from the GATK resource bundle. In this case hapmap_3.3.b37.vcf.gz from your bundle has hapmap_3.3.b37.vcf.idx.gz in the same directory. I suspect this is because my input VCF file is tabix indexed something in GATK has decided that everything else must be. Is there any way to override this? I'm guessing it might be something to do with tribbles? But I can't seem to find the relevant bit of documentation that explains this. Thanks, martin

idx format specification or code

Where would be the best place to find idx format specifications and/or the Java code that handles reading and writing idx files. Thanks!