VariantFiltration isn't working
REQUIRED for all errors and issues:
a) GATK version used: v.4.4.0
b) Exact command used:
srun apptainer exec $GATK gatk VariantFiltration \
-R /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/PauloM_Analysis/Genome/GRCm39.primary_assembly.genome.fa \
-V /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/GATK/"$pair1"_snps.vcf.gz \
-O /mnt/nfs/lobo/JBARATA-NFS/paulo.mendonca/GATK/"$pair1"_filtered_snps.vcf.gz \
--filter-expression "QD < 2.0" --filter-name "QD_filter" \
--filter-expression "FS > 60.0" --filter-name "FS_filter" \
--filter-expression "MQ < 40.0" --filter-name "MQ_filter" \
--filter-expression "SOR > 4.0" --filter-name "SOR_filter" \
--filter-expression "MQRankSum < -12.5" --filter-name "MQRankSum_filter" \
--filter-expression "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum_filter"
c) Entire program log:
13:47:52.608 WARN JexlEngine - ![0,14]: 'ReadPosRankSum < -8.0;' undefined variable ReadPosRankSum
It appears this.
However:
chr1 7719943 . C T 35.64 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.981;DP=7;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.10;MQRankSum=-1.981;QD=5.09;ReadPosRankSum=1.180;SOR=0.446
This variant was marked ha pass and doesn't have right QD, ReadPosRankSum , FS, SOR, MQRANKSUM, why does it pass? Can someone explain me please.
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Those values looked all fine to me so this variant is correctly marked as PASS.
Looking at your filters
QD = 5.09 which is greater than 2.0 --> PASSED
FS = 0.0 which is less than 60.0 --> PASSED
MQ = 56.10 greater than 40 --> PASSED
SOR = 0.446 which is less than 4.0 --> PASSED
MQRankSum = -1.981 which is greater than -12.5 --> PASSED
so on..
Those filters are designed to tag variants with extreme biasses for those terms and values are derived from VQSR profiles that we had in the past. They are good suggestions to begin with but if you have reservations for more filters then you may need to experiment with those values and see how it fares.
Regards.
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