All reads filtered out

xin.huangxin.huang Washington, DCMember

Dear GATK Team,

I was trying to use joint calling by GATK, first I aligned the RNA-Seq reads to a genome reference using HISAT, and the overall alignment rate was over 70% with over 50% read pairs mapping concordantly only once. Then I marked the duplicates using Picard. The command I used for individual libraries is: java -jar /path/to/GenomeAnalysisTK.jar -T HaplotypeCaller -R -I --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o . And the terminal output is:
INFO 08:37:27,359 ProgressMeter - Total runtime 2993.19 secs, 49.89 min, 0.83 hours
INFO 08:37:27,359 MicroScheduler - 26025551 reads were filtered out during the traversal out of approximately 26025551 total reads (100.00%)
INFO 08:37:27,360 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 08:37:27,360 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 08:37:27,360 MicroScheduler - -> 8905798 reads (34.22% of total) failing HCMappingQualityFilter
INFO 08:37:27,361 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 08:37:27,361 MicroScheduler - -> 17119753 reads (65.78% of total) failing MappingQualityUnavailableFilter
INFO 08:37:27,361 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
INFO 08:37:27,362 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter

Could you provide some guidance to try figuring out what could be the issue here?

Many thanks,

Xin

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