I have human RNA-seq data: paired-end reads (2x150bp) aligned with STAR. I tried to run HaplotypeCaller with usual parameters:
`gatk HaplotypeCaller -R GRCh38.primary_assembly.genome.fa -I S_1_rg_added.bam -stand-call-conf 20.0 -O $S_1.vcf`
Resulting vcf contains all the usual header lines but nothing else, no actual variants. End of the program's output log looks like this:
00:04:44.732 INFO ProgressMeter - chrM:1501 7.7 10294250 1332911.1
00:04:48.991 INFO HaplotypeCaller - 62395557 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
62395557 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter)
62395557 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
62395557 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
62395557 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
62395557 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
62395557 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter)
62395557 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter)
10670778 read(s) filtered by: MappingQualityReadFilter
51724779 read(s) filtered by: MappingQualityAvailableReadFilter
00:04:48.992 INFO ProgressMeter - KI270757.1:71101 7.8 10332600 1325689.4
00:04:48.992 INFO ProgressMeter - Traversal complete. Processed 10332600 total regions in 7.8 minutes.
00:04:49.000 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
00:04:49.000 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
00:04:49.000 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
00:04:49.000 INFO HaplotypeCaller - Shutting down engine
[April 24, 2019 12:04:49 AM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 7.82 minutes.
Runtime.totalMemory()=3580887040
Any ideas of what could be wrong here?
Thanks!
`gatk HaplotypeCaller -R GRCh38.primary_assembly.genome.fa -I S_1_rg_added.bam -stand-call-conf 20.0 -O $S_1.vcf`
Resulting vcf contains all the usual header lines but nothing else, no actual variants. End of the program's output log looks like this:
00:04:44.732 INFO ProgressMeter - chrM:1501 7.7 10294250 1332911.1
00:04:48.991 INFO HaplotypeCaller - 62395557 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
62395557 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND GoodCigarReadFilter)
62395557 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
62395557 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
62395557 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
62395557 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
62395557 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappedReadFilter)
62395557 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter)
10670778 read(s) filtered by: MappingQualityReadFilter
51724779 read(s) filtered by: MappingQualityAvailableReadFilter
00:04:48.992 INFO ProgressMeter - KI270757.1:71101 7.8 10332600 1325689.4
00:04:48.992 INFO ProgressMeter - Traversal complete. Processed 10332600 total regions in 7.8 minutes.
00:04:49.000 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
00:04:49.000 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
00:04:49.000 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 0.00 sec
00:04:49.000 INFO HaplotypeCaller - Shutting down engine
[April 24, 2019 12:04:49 AM EDT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 7.82 minutes.
Runtime.totalMemory()=3580887040
Any ideas of what could be wrong here?
Thanks!