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Exome seq analysis: MESSAGE: I/O error loading or writing tribble index file

arunkumar.gparunkumar.gp IndiaMember
edited November 2015 in Ask the GATK team

Dear all,

I am trying to analyse a publicly available human exome seq dataset. I am stuck at the stage to "create target list of intervals to be realigned". I used the "human_g1k_v37.fasta" avaibale from GATK bundle as the reference in BWA mapping. After creating the BAM files, to create a VCF file, I want to follow the GATK best practice. Here is what I did:

BWA:
$ ~/BWA/bwa-0.7.12/bwa aln -t 12 ~/Reference/HG_37/human_g1k_v37.fasta ~/BWA/bwa-0.7.12/ERR445410_1.fastq > ERR445410_1.sai

$ ~/BWA/bwa-0.7.12/bwa aln -t 12 ~/Reference/HG_37/human_g1k_v37.fasta ~/BWA/bwa-0.7.12/ERR445410_2.fastq > ERR445410_2.sai

$ ~/BWA/bwa-0.7.12/bwa sampe ~/Reference/HG_37/human_g1k_v37.fasta ~/BWA/bwa-0.7.12/ERR445410_1.sai ~/BWA/bwa-0.7.12/ERR445410_2.sai ~/BWA/bwa-0.7.12/ERR445410_1.fastq ~/BWA/bwa-0.7.12/ERR445410_2.fastq > ERR445410.sam

samtools and remove all unmapped reads:
samtools view -bF 4 ERR445410.bam > ERR445410_unMpdfltr.bam

Sort BAM file to coordinate order
$ java -jar picard.jar SortSam INPUT=ERR445410_unMpdFltr.bam OUTPUT=ERR445410_cord_srt.bam SORT_ORDER=coordinate

Picard command to mark duplicates:
$ java -jar picard.jar MarkDuplicates INPUT=ERR445410_cord_srt.bam OUTPUT=ERR445410_dedup_reads.bam METRICS_FILE=metrics.txt

Picard command to index the BAM file:
$ java -jar picard.jar BuildBamIndex INPUT=ERR445410_dedup_reads.bam

Change the read group header in picard:
java -jar picard.jar AddOrReplaceReadGroups \
INPUT=ERR445410_dedup_reads.bam \
OUTPUT=ERR445410_dedup_reads_RG.bam \
RGLB=whatever \
RGPL=illumina \
RGPU=whatever \
RGSM=whatever

Picard command to re-index the BAM file:
$ java -jar picard.jar BuildBamIndex INPUT=ERR445410_dedup_reads_RG.bam

GATK
Create a target list of intervals to be realigned:
java -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
-I ERR445410_dedup_reads.bam \
-known Mills_and_1000G_gold_standard.indels.b37.vcf \
-o realignment_targets.list

When I entered the above mentioned GATK command, I get the following error message:

ERROR MESSAGE: I/O error loading or writing tribble index file

I am using CYGWIN for running all the programs. My OS is WIn10. I request someone to kindly help me trouble shoot.

Thanks in advance.

Regards,
G. Arun Kumar

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