When using CombineVariants, my variants get a FILTER value of either PASS or LowQual. Would it be possible to add an option to CombineVariants which prevents the FILTER value to be set to PASS? Otherwise I have to do some file processing before I run ApplyRecalibration further downstream. It would be great if this was a feature of all walkers and not just VariantFiltration. I'm not sure if the forum is the right place for feature requests. Happy to use Bugzilla or similar instead. Thanks.
I have completed filtering my SNP data using VariantFiltration, and now I want to use SelectVariants to output all calls marked "PASS" in the FILTER field. I used the following script, but only the header information writes to the output file.
java -Xmx20g -jar GenomeAnalysisTK.jar -T SelectVariants -R HC.fa --variant HC.SNPs.filtered.vcf -select "FILTER == 'PASS'" -o HC.SNPs.passed.vcf
My input file contains many records that should evaluate as true. Any idea why this doesn't this work?
Hi all,
I'm currently analysing non-human mammalian whole genome data (>30x). No previous variants databases are available.
I'm currently in the VariantFiltration step. I came around the following command which is used for human data, and I'm wondering if it will be good for non-human data:
java -Xmx10g -jar GenomeAnalysisTK.jar \
-R [reference.fasta] \
-T VariantFiltration \
--variant [input.recalibrated.vcf] \
-o [recalibrated.filtered.vcf] \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "HARD_TO_VALIDATE" \
--filterExpression "DP < 5 " \
--filterName "LowCoverage" \
--filterExpression "QUAL < 30.0 " \
--filterName "VeryLowQual" \
--filterExpression "QUAL > 30.0 && QUAL < 50.0 " \
--filterName "LowQual" \
--filterExpression "QD < 1.5 " \
--filterName "LowQD" \
--filterExpression "SB > -10.0 " \
--filterName "StrandBias"
I would appreciate your thoughts on this matter.
Thank you very much!
Sagi
Hi, I would like to perform base quality score recalibration on only the reads that have the "properly aligned" bit (0x2) set in the FLAG column of the SAM format. Ideally, I would like to use the --read_filter argument. Below is some code that does this to my satisfaction with the PrintReads walker of GATK 2 lite. However, GATK 2 lite does not support base quality score recalibration table creation. Is there any way someone could add the code to the GATK 2 full version?
I am not sure why, but the code seems to only work with the System.out.println() line.
Thanks, Winni
/* * code written by Kiran Garimella */
package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMRecord;
public class ProperPairFilter extends ReadFilter { @Override public boolean filterOut(SAMRecord samRecord) { System.out.println(samRecord.getProperPairFlag()); return !samRecord.getProperPairFlag(); } }