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Constant reopenning of VCF file in GATK
we have encountered the following issue on GATK (version 2.3).
In the command lines:
1) java -Xmx8g -jar <GenomeAnalysisTK.jar> -rf BadCigar -stand_call_conf 20 -stand_emit_conf 10 -dcov 50 -R <file.fasta> -I <file.bam> --dbsnp <file.issue.vcf> -metrics <file.metrics> -o .vcf -glm BOTH -L <file.bed> -nt 3 ;
2) java -Xmx4g -jar <GenomeAnalysisTK.jar> -T VariantAnnotator -rf BadCigar -R <file.fasta> -I <file.bam> -o <file.vcf> -G StandardAnnotation -A AlleleBalanceBySample -A DepthPerAlleleBySample -A MappingQualityZeroBySample --variant <file.issue.vcf> -L <file.bed>
3) java -Xmx4g -jar <GenomeAnalysisTK.jar> -T VariantFiltration -rf BadCigar -R <file.fasta> -o <file.vcf> --filterExpression 'DP<6 || FS>25' --filterName 'PFMFilter' --variant <file.issue.vcf> -L <file.bed> ;
the file <file.issue.vcf> may be constantly reopened. On our cases, this nearly always occurs in (1) and regularly occurs in (2) and (3).
For detecting the issue we used : strace -e trace=file -f
Are you aware of it ?
Would you mind fixing it ?