(This has been x-posted to the GATK forum.)

I have a file called rawSnps.vcf, which I've been trying to filter through the VariantFiltration Walker. The command I've been using is as follows:

/usr/java/latest/bin/java \
  -Xmx2g \
  -jar ~/bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
  -T VariantFiltration \
  -R /home/rothlab/agopal/bin/bowtie2-2.2.3/indexes/s_cerevisiae.fa \
  -V Papi_C02_1/rawSnps.vcf \
  --filterExpression "QD < 2 || FS > 60 || MQ < 40 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8" \
  --filterName "snpfilter" \
  -o Papi_C02_1/filtered_snps.vcf -allowPotentiallyMisencodedQuals

I noticed that this wasn't working, so I switched to a more simple command, like this:

/usr/java/latest/bin/java \
  -Xmx2g \
  -jar ~/bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar \
  -T VariantFiltration \
  -R /home/rothlab/agopal/bin/bowtie2-2.2.3/indexes/s_cerevisiae.fa \
  -V rawSnps.vcf \
  --filterExpression "MQ < 30" \
  --filterName "snpfilter" \
  -o filtered_snps_test.vcf \
  -allowPotentiallyMisencodedQuals

However, that isn't working either.

The output I get from GATK looks like this:

/usr/java/latest/bin/java -Xmx2g -jar ~/bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T VariantFiltration -R /home/rothlab/agopal/bin/bowtie2-2.2.3/indexes/s_cerevisiae.fa -V rawSnps.vcf --filterExpression "MQ < 30" --filterName "snpfilter" -o filtered_snps_test.vcf -allowPotentiallyMisencodedQuals
INFO  10:03:14,434 HelpFormatter - --------------------------------------------------------------------------------
INFO  10:03:14,436 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
INFO  10:03:14,437 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  10:03:14,437 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  10:03:14,442 HelpFormatter - Program Args: -T VariantFiltration -R /home/rothlab/agopal/bin/bowtie2-2.2.3/indexes/s_cerevisiae.fa -V rawSnps.vcf --filterExpression MQ < 30 --filterName snpfilter -o filtered_snps_test.vcf -allowPotentiallyMisencodedQuals
INFO  10:03:14,445 HelpFormatter - Executing as agopal@guru-int.mshri.on.ca on Linux 2.6.32-431.11.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13.
INFO  10:03:14,445 HelpFormatter - Date/Time: 2015/05/04 10:03:14
INFO  10:03:14,445 HelpFormatter - --------------------------------------------------------------------------------
INFO  10:03:14,445 HelpFormatter - --------------------------------------------------------------------------------
INFO  10:03:15,216 GenomeAnalysisEngine - Strictness is SILENT
INFO  10:03:15,308 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  10:03:15,439 GenomeAnalysisEngine - Preparing for traversal
INFO  10:03:15,440 GenomeAnalysisEngine - Done preparing for traversal
INFO  10:03:15,440 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  10:03:15,441 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  10:03:15,441 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
INFO  10:03:17,682 ProgressMeter -            done      7942.0     2.0 s       4.7 m       99.9%     2.0 s       0.0 s
INFO  10:03:17,682 ProgressMeter - Total runtime 2.24 secs, 0.04 min, 0.00 hours
INFO  10:03:18,554 GATKRunReport - Uploaded run statistics report to AWS S3

i.e., you there is no error report. However, when I manually look at filtered_snps_test.vcf, I can see that many SNPs that have a MQ value below 30 (or 40, if that's what I've used) have still been passed in the filter.

I've also done a raw line-count of rawSnps.vcf and filtered_snps_test.vcf, and starting at the #CHROM position, both line counts are the same.

I'm not sure what's going on here. You can see both files here:

rawSnps.vcf: https://www.dropbox.com/s/868kkpna5n315r0/filtered_snps_test.vcf?dl=0

filtered_snps_test.vcf: https://www.dropbox.com/s/868kkpna5n315r0/filtered_snps_test.vcf?dl=0

Any help would be much appreciated.

Thanks!