GATK filterExpression multiplication (*) mistaken for wildcard

tsecogen · 03-30-2013, 10:18 AM

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

davidblaney · 03-31-2013, 04:04 AM

Hi,

Have you tried backslash before it:

(1.0 \* DP)

or using single quotes around the expression?

tsecogen · 04-01-2013, 07:34 AM

Thanks for the suggestions but unfortunately neither of them work. I still had the same problem with * being recognized as a wild card.

mastal · 04-01-2013, 07:45 AM

Have you tried MQ0 / DP > 0.1?

Obviously this will only work for cases when you want to multiply DP by 1.0.

tsecogen · 04-04-2013, 06:39 AM

Thanks for the thought, but DP (Depth of Coverage) changes for every SNP so it is not safe to assume it is 1 or any other number for all SNPs.

In the end I just transfered the input files to my imac to run that piece of the code. Not the most elegant work around but at least it allows me to move forward.

Thanks.

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03-30-2013, 10:18 AM	#1
tsecogen Member Location: Birmingham, AL Join Date: Mar 2013 Posts: 10	*GATK filterExpression multiplication () mistaken for wildcard** 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

04-01-2013, 07:45 AM	#4
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 667	*GATK filterExpression multiplication () mistaken for wildcard** Have you tried MQ0 / DP > 0.1? Obviously this will only work for cases when you want to multiply DP by 1.0.

03-31-2013, 04:04 AM	#2
davidblaney Member Location: Oxford, UK Join Date: Nov 2011 Posts: 17	Hi, Have you tried backslash before it: (1.0 \* DP) or using single quotes around the expression?

04-01-2013, 07:34 AM	#3
tsecogen Member Location: Birmingham, AL Join Date: Mar 2013 Posts: 10	Thanks for the suggestions but unfortunately neither of them work. I still had the same problem with * being recognized as a wild card.

04-04-2013, 06:39 AM	#5
tsecogen Member Location: Birmingham, AL Join Date: Mar 2013 Posts: 10	Thanks for the thought, but DP (Depth of Coverage) changes for every SNP so it is not safe to assume it is 1 or any other number for all SNPs. In the end I just transfered the input files to my imac to run that piece of the code. Not the most elegant work around but at least it allows me to move forward. Thanks.