Hi. I am using GATK for SNP identification and I have come across a problem when filtering the SNPs, where the * for multiplication (see code below) is being mistaken for a wildcard for all files in the folder. Does anyone have a solution for the * to be recognized as a multiplication and not a wildcard? Thank you!
System: Unix higher performance cluster
Code:
java -Xmx16g -jar GenomeAnalysisTK.jar \
-T VariantFiltration \
-R MtGenome_sections.fasta \
--variant GATK_4_Indel_filtered_Q30.vcf \
-o GATK_5_analysis_ready_Q30.vcf \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "HARD_TO_VALIDATE" \
--filterExpression "SB >= -1.0" \
--filterName "StrandBiasFilter" \
--filterExpression "QUAL < 10" \
--filterName "QualFilter" \
--filterExpression "QUAL < 30.0 || QD < 5.0 || HRun > 5 || SB > -0.10" \
--filterName GATKStandard
System: Unix higher performance cluster
Code:
java -Xmx16g -jar GenomeAnalysisTK.jar \
-T VariantFiltration \
-R MtGenome_sections.fasta \
--variant GATK_4_Indel_filtered_Q30.vcf \
-o GATK_5_analysis_ready_Q30.vcf \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "HARD_TO_VALIDATE" \
--filterExpression "SB >= -1.0" \
--filterName "StrandBiasFilter" \
--filterExpression "QUAL < 10" \
--filterName "QualFilter" \
--filterExpression "QUAL < 30.0 || QD < 5.0 || HRun > 5 || SB > -0.10" \
--filterName GATKStandard
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