GATK Variant Filtration undefined variable
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8.0
b) Exact command used: gatk VariantFiltration -V Input_SNP.vcf -filter "QD < 2.0" --filter-name "QD2" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" -filter "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" -filter "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" -O Output_SNP_filtered.vcf
c) Entire error log:
12:55:44.734 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/root/Work/GenomeINDIA_Data/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Oct 21, 2021 12:55:50 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
12:55:50.040 INFO VariantFiltration - ------------------------------------------------------------
12:55:50.040 INFO VariantFiltration - The Genome Analysis Toolkit (GATK) v4.1.8.0
12:55:50.040 INFO VariantFiltration - For support and documentation go to https://software.broadinstitute.org/gatk/
12:55:50.041 INFO VariantFiltration - Executing as root@localhost.localdomain on Linux v3.10.0-514.el7.x86_64 amd64
12:55:50.041 INFO VariantFiltration - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-b08
12:55:50.041 INFO VariantFiltration - Start Date/Time: October 21, 2021 12:55:44 PM IST
12:55:50.041 INFO VariantFiltration - ------------------------------------------------------------
12:55:50.041 INFO VariantFiltration - ------------------------------------------------------------
12:55:50.041 INFO VariantFiltration - HTSJDK Version: 2.22.0
12:55:50.042 INFO VariantFiltration - Picard Version: 2.22.8
12:55:50.042 INFO VariantFiltration - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:55:50.042 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:55:50.042 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:55:50.042 INFO VariantFiltration - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:55:50.042 INFO VariantFiltration - Deflater: IntelDeflater
12:55:50.042 INFO VariantFiltration - Inflater: IntelInflater
12:55:50.042 INFO VariantFiltration - GCS max retries/reopens: 20
12:55:50.042 INFO VariantFiltration - Requester pays: disabled
12:55:50.042 INFO VariantFiltration - Initializing engine
12:55:50.272 INFO FeatureManager - Using codec VCFCodec to read file file:///root/Work/GenomeINDIA_Data/Vcf_files_2020/1011GI_ApplyVQSR/chr22/1011GI_ApplyBQSR_chr22_SNP.vcf
12:55:50.357 INFO VariantFiltration - Done initializing engine
12:55:50.622 INFO ProgressMeter - Starting traversal
12:55:50.622 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
12:55:50.650 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
12:55:50.650 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
12:55:50.652 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
12:55:50.652 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
12:55:50.656 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:02.680 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:02.680 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:02.680 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:02.724 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:02.724 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:02.892 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:02.892 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:03.355 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:03.355 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:03.355 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:03.355 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:03.700 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:03.846 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:03.846 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:03.895 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:03.895 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:03.950 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:03.950 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:04.030 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:04.030 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:04.065 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:04.066 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:04.303 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:04.303 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:04.415 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:04.415 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:04.430 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
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13:01:48.151 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.152 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.152 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.153 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.153 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.238 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.238 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.238 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.265 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.265 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.275 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.275 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.445 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.446 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.446 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.447 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.448 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.526 INFO ProgressMeter - chr22:50711881 6.0 637000 106788.7
13:01:48.732 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.732 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:48.872 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:48.872 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.453 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.453 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.525 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.525 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.526 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.526 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.527 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.527 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.544 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.544 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.553 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.554 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.555 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.555 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.650 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.650 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.652 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.653 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.653 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.654 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.656 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.656 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.658 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.660 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.660 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.662 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.662 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.666 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.666 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.668 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.668 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.668 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.668 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.670 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
13:01:49.670 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.670 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.671 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.671 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
13:01:49.671 INFO ProgressMeter - chr22:50771160 6.0 638902 106765.7
13:01:49.672 INFO ProgressMeter - Traversal complete. Processed 638902 total variants in 6.0 minutes.
13:01:49.698 INFO VariantFiltration - Shutting down engine
[October 21, 2021 1:01:49 PM IST] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 6.08 minutes.
Runtime.totalMemory()=1533542400
Using GATK jar /root/Work/GenomeINDIA_Data/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /root/Work/GenomeINDIA_Data/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar VariantFiltration -V 1011GI_ApplyBQSR_chr22_SNP.vcf -filter QD < 2.0 --filter-name QD2 -filter QUAL < 30.0 --filter-name QUAL30 -filter SOR > 3.0 --filter-name SOR3 -filter FS > 60.0 --filter-name FS60 -filter MQ < 40.0 --filter-name MQ40 -filter MQRankSum < -12.5 --filter-name MQRankSum-12.5 -filter ReadPosRankSum < -8.0 --filter-name ReadPosRankSum-8 -O 1011GI_ApplyBQSR_chr22_SNP_filtered.vcf
This is ##INFO lines from input:
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=GQ_MEAN,Number=1,Type=Float,Description="Mean of all GQ values">
##INFO=<ID=GQ_STDDEV,Number=1,Type=Float,Description="Standard deviation of all GQ values">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=LikelihoodRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref haplotype likelihoods">
##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples">
##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants">
##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=RAW_MQandDP,Number=2,Type=Integer,Description="Raw data (sum of squared MQ and total depth) for improved RMS Mapping Quality calculation. Incompatible with deprecated RAW_MQ formulation.">
##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
##INFO=<ID=hiConfDeNovo,Number=1,Type=String,Description="High confidence possible de novo mutation (GQ >= 20 for all trio members)=[comma-delimited list of child samples]">
##INFO=<ID=loConfDeNovo,Number=1,Type=String,Description="Low confidence possible de novo mutation (GQ >= 10 for child, GQ > 0 for parents)=[comma-delimited list of child samples]">
I have seen these same issues from different users, but I couldn't found proper solution.
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These messages are most likely occurring at locations in your file where there is no value for ReadPosRankSum or MQRankSum. However, these are just warning messages stating that VariantFiltration won't be able to filter for those annotations at sites where they aren't present. These aren't actual error messages and it seems that the tool is still finishing properly, so you should be able to ignore the warnings. Please let me know if this helps answer your question.
Kind regards,
Pamela
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Hi Pamela Bretscher,
Thanks for your reply. Here I am providing a variant line, which has the value of ReadPosRankSum or MQRankSum. Also, I am not seeing any differences after applying this filtration. So could you please explain to me why this filtration is not applied to my input file?
Example line:
chr22 10536709 . T C 153717.48 VQSRTrancheSNP99.70to99.80 AC=520;AF=0.633;AN=822;AS_UNIQ_ALT_READ_COUNT=0;BaseQRankSum=-1.072e+00;DP=4929;ExcessHet=-0.0000;FS=5.776;GQ_MEAN=31.25;GQ_STDDEV=25.93;InbreedingCoeff=0.4864;MBQ=0,0;MFRL=0,0;MLEAC=1519;MLEAF=1.00;MMQ=60,60;MPOS=50;MQ=32.42;MQ0=0;MQRankSum=0.529;NCC=600;NCount=0;NEGATIVE_TRAIN_SITE;QD=33.68;ReadPosRankSum=1.30;SOR=0.013;VQSLOD=-1.995e+00;culprit=DP GT:AD:AF:DP:F1R2:F2R1:GQ:PL 1/1:0,0:1.00:0:0,0:0,0:54:624,54,0
Regards
Krithika S
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Thank you for providing this example line. Are there other lines where MQRankSum and ReadPosRankSum are not present? The values are present in this particular line but the warning messages are likely coming from lines where the values are not there. These values can't be calculated at sites where there are no heterozygous individuals, but it should not affect filtration. In regards to the filtration not being applied, do you mean that VariantFiltration is not annotating any variants as PASS/failing or that filtration is not being applied for these two annotations?
Kind regards,
Pamela
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Hi Pamela Bretscher,
Thanks for your reply. Could you please explain me, how I can check whether VariantFiltration is applied for my data?
Because there are 742,973 variants present before applying VariantFiltration. After running the above command, the same number of variants were presents in the output .vcf file. That's the reason, I am wondering to know whether filtration is applied or not applied to my input.
Regards,
Krithika S
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The VariantFiltration tool will annotate each variant either as PASS (if it passes all filter criteria) or it will annotate the variant by changing the FILTER field to the reason why the variant failed filtration. However, all of the variants will still be kept in the VCF file unless you specify that they should be removed. Therefore, it makes sense that you still have the same number of variants in the output file, but they should now be annotated based on if they passed or failed the applied filters. You can either check the output file for the annotations or specify that you would like the failing variants to be removed to check whether VariantFiltration is being applied properly. More information can be found in the tool documentation.
Kind regards,
Pamela
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Hi Pamela,
Thank you for your clarification. I have given specific parameters in my command for excluding, for example, QD <2.0, SOR > 3.0, MQ < 40.0 etc.
In my input, there are variants that have MQ < 30. So I am expecting that should remove after using this filtration. But I am getting the same number of variants. Kindly help me resolve these issues.
Exact command used: gatk VariantFiltration -V Input_SNP.vcf -filter "QD < 2.0" --filter-name "QD2" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" -filter "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" -filter "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" -O Output_SNP_filtered.vcf
Thank you
Regards
Krithika S
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These filtering parameters do not actually remove variants from your VCF file if they do not pass the filters. Rather, these variants will just be labeled with why they fail your specifications in the output VCF. If variants pass all filters, they will be labeled as PASS, but all of the variants will still be present in the VCF. Could you look at your output VCF file or include a few lines of it here to see if the variants are properly labeled (e.g. chr2 213455 G GTT 34449.7 PASS)?
Kind regards,
Pamela
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