I am using Unified Genotyper of (GATK) to call variations from my exome dataset. Before calling variations I realigned and recalibrated the dataset as suggested by GATK pipeline. Surprisingly for one of the samples unified genotyper is running for required time and ends without any error BUT the vcf file generated has no called variations. The output only contains initial headers of vcf file and nothing else. The log file shows following:
INFO 04:59:00,484 UnifiedGenotyper - Visited bases 3137891381 INFO 04:59:00,484 UnifiedGenotyper - Callable bases 2860850500 INFO 04:59:00,485 UnifiedGenotyper - Confidently called bases 2674460611 INFO 04:59:00,485 UnifiedGenotyper - % callable bases of all loci 91.171 INFO 04:59:00,485 UnifiedGenotyper - % confidently called bases of all loci 85.231 INFO 04:59:00,485 UnifiedGenotyper - % confidently called bases of callable loci 93.485 INFO 04:59:00,485 UnifiedGenotyper - Actual calls made 0 INFO 04:59:00,486 TraversalEngine - Total runtime 13136.39 secs, 218.94 min, 3.65 hours INFO 04:59:00,486 TraversalEngine - 160540 reads were filtered out during traversal out of 34176517 total (0.47%) INFO 04:59:00,486 TraversalEngine - -> 71636 reads (0.21% of total) failing BadMateFilter INFO 04:59:00,486 TraversalEngine - -> 88904 reads (0.26% of total) failing UnmappedReadFilter INFO 04:59:19,240 GATKRunReport - Uploaded run statistics report to AWS S3
Upon inspection, I found that complete vcf file is being generated before recalibration , but after recalibration it is malformed!
Need help on this!!
Thanks in advance.