Hi, I'm a newer to Bioinfo, and I have some questions in GATK variant calling.
I'm working on germline variant calling from human exome sequencing data.I have two samples ,and I use the same GATK pipeline to call variants. One can be down successfully, but the other was failed at the HaplotypeCaller step.
The HaplotypeCaller log message: Total compute time in PairHMM computeLikelihoods() : 0.0
INFO 09:49:25,501 HaplotypeCaller - Ran local assembly on 37 active regions
INFO 09:49:25,634 ProgressMeter - done 3.10e+09 8.5 h 9.0 s 100.0% 8.5 h 1.0 s
INFO 09:49:25,634 ProgressMeter - Total runtime 30522.59 secs, 508.71 min, 8.48 hours
INFO 09:49:25,634 MicroScheduler - 69094228 reads were filtered out during the traversal out of approximately 128324603 total reads (53.84%)
INFO 09:49:25,635 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 09:49:25,635 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 09:49:25,635 MicroScheduler - -> 68909447 reads (53.70% of total) failing HCMappingQualityFilter
INFO 09:49:25,636 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 09:49:25,636 MicroScheduler - -> 0 reads (0.00strong text% of total) failing MappingQualityUnavailableFilter
INFO 09:49:25,636 MicroScheduler - -> 184781 reads (0.14% of total) failing NotPrimaryAlignmentFilter
INFO 09:49:25,636 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 09:49:34,090 GATKRunReport - Uploaded run statistics report to AWS S3
I think it is strange that 53.70% of total reads failed the HCMappingQualityFilter. And another question is the output vcf file is really small (only 24KB), it seems the file is incomplete, however, the HaplotypeCaller stopped variant calling without an error message, and directly run the next step.
This is the error massage at VariantRecalibrator step: ##### ERROR MESSAGE: Bad input: Values for MQRankSum annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations.
Does anyone have met this error before? what should I do to solve this problem, could anyone give me some advice ？ Thanks a lot!
