VariantFiltration failed
GATK version used: gatk-4.4.0
I used this command for filtration and got an error
java -jar gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar VariantFiltration -R ../Ref_7b_fa/GRCg7b.dna_rm.toplevel.fa -V SNP.vcf -O SNp_filtered.vcf \
-filter-name "QD_filter" -filter "QD < 2.0" \
-filter-name "QUAL30" -filter "QUAL < 30.0" \
-filter-name "FS_filter" -filter "FS > 60.0" \
-filter-name "MQ_filter" -filter "MQ < 40.0" \
-filter-name "SOR_filter" -filter "SOR > 4.0" \
-filter-name "MQRankSum_filter" -filter "MQRankSum < -12.5" \
-filter-name "ReadPosRankSum_filter" -filter "ReadPosRankSum < -8.0" \
-genotype-filter-expression "DP < 10" \
-genotype-filter-name "DP_filter" \
-genotype-filter-expression "GQ < 10" \
-genotype-filter-name "GQ_filter"
21:05:33.882 WARN JexlEngine - ![0,9]: 'MQRankSum < -12.5;' undefined variable MQRankSum
21:05:33.882 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
After that, i checked the file to show the values of ReadPosRankSum and ReadPosRankSum, and found all to be equal 0
- then I checked previous steps also (GenotypeGVCFs , SelectVariants ) also found the values of ReadPosRankSum and ReadPosRankSum, equal 0
- I am stuck on variant calling for long time , please help me to detect the error
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This is just a warning message that particular variant contexts do not have those variables within. Tool works just as fine and will skip those variant sites for those filters. Not all variants will have all parameters set.
Regards.
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So, I can discard these two parameters and continue
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No you don't have to. You can leave it as is and tool will work accordingly.
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