SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Wildcard Nucleotide Bases hyjkim Bioinformatics 5 11-15-2015 01:06 PM
About GATK bewlib Bioinformatics 1 11-03-2012 08:00 PM
internal multiplication of low-complexity regions during cluster building ein_io Illumina/Solexa 0 05-09-2012 04:38 PM
GATK ReadCounts mikyi General 0 08-26-2011 03:35 PM
GATK help! adaptivegenome Bioinformatics 0 01-17-2011 08:01 PM

Reply
 
Thread Tools
Old 03-30-2013, 10:18 AM   #1
tsecogen
Member
 
Location: Birmingham, AL

Join Date: Mar 2013
Posts: 10
Default 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
tsecogen is offline   Reply With Quote
Old 03-31-2013, 04:04 AM   #2
davidblaney
Member
 
Location: Oxford, UK

Join Date: Nov 2011
Posts: 17
Default

Hi,

Have you tried backslash before it:

(1.0 \* DP)

or using single quotes around the expression?
davidblaney is offline   Reply With Quote
Old 04-01-2013, 07:34 AM   #3
tsecogen
Member
 
Location: Birmingham, AL

Join Date: Mar 2013
Posts: 10
Default

Thanks for the suggestions but unfortunately neither of them work. I still had the same problem with * being recognized as a wild card.
tsecogen is offline   Reply With Quote
Old 04-01-2013, 07:45 AM   #4
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default 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.
mastal is offline   Reply With Quote
Old 04-04-2013, 06:39 AM   #5
tsecogen
Member
 
Location: Birmingham, AL

Join Date: Mar 2013
Posts: 10
Default

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.
tsecogen is offline   Reply With Quote
Reply

Tags
filterexpression, gatk, wildcard

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:27 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO