I'm currently trying to call SNP on several samples (8 bam, 1 pseudoref) and 75.15% of my reads have failed the DuplicateReadFilter. I tried to disable this filter with "-drf DuplicateRead" in the command line but that error came up (drf not defined).
Hi, I am processing exome data and about 10~20% of reads failed DuplicateReadFilter during HaplotypeCaller step. For some samples, more than 70% failed this step, so I want to know usually what percentage of reads fail DuplicateReadFilter. Maybe a silly question, but these percentages increase as the depth increase?
Command and Result for HaplotypeCaller are as below.
java -Xms2G -Xmx4G -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R ucsc.hg19.fasta -I S1.recalrealndup.bam -L targetedregions.bed -o S1.g.vcf -ERC GVCF -nct 2
INFO 05:56:26,329 MicroScheduler - 71604429 reads were filtered out during the traversal out of approximately 94595522 total reads (75.70%) INFO 05:56:26,329 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter INFO 05:56:26,330 MicroScheduler - -> 67530996 reads (71.39% of total) failing DuplicateReadFilter INFO 05:56:26,330 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 05:56:26,330 MicroScheduler - -> 4073433 reads (4.31% of total) failing HCMappingQualityFilter INFO 05:56:26,331 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 05:56:26,331 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 05:56:26,331 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 05:56:26,331 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter INFO 05:56:30,377 GATKRunReport - Uploaded run statistics report to AWS S3
Hi, I am using GATK HC to identify variants in a target region of about 23kb with very deep sequencing. I get this message during HC that 99.76% of reads failing DuplicateReadFilter. This means that a lot of my reads are being thrown out and hence I am not getting correct variant calls.
First, is GATK HC an appropriate tool to call variants in such a small region with deep sequencing (more than 100X)? Second, how can I rectify this error of 99% reads failing DuplicateReadFilter?
My understanding of DuplicateReadFilter is that is removes PCR duplicates (ie: identical reads that map to the same location in the genome). Is there a way to prevent UnifiedGenotyper from using this filter?
Many of my 'duplicate' reads are not really duplicates. I have 50bp single ended yeast RNA-seq data, and 10 samples/lane results in highly over-sampled data. Removing duplicates results in an undercounting of reads at the most highly expressed genes, and therefore an increased number of sub-clonal variants at these genes (because the reads from the major clonal population are discarded, but reads of sub-clonal populations are kept because they have a different sequence). At least I think that is what is happening.
Hello GATK team,
BaseRecalibrator applies the filters: DuplicateReadFilter MappingQualityZeroFilter I've noticed that in the bam after PrintReads, most of those reads indeed filtered out, but few of them were left - about 2% reads that were marked as dups by picard, and 4% reads with a mapping quality zero.
What exactly happens when a tool applies a filter?
Filter out duplicate reads.
I just noticed something odd about GATK read counts. Using a tiny test data set, I generated a BAM file with marked duplicates.
This is the output for samtools flagstat:
40000 + 0 in total (QC-passed reads + QC-failed reads) 63 + 0 duplicates 38615 + 0 mapped (96.54%:-nan%) 40000 + 0 paired in sequencing 20000 + 0 read1 20000 + 0 read2 37764 + 0 properly paired (94.41%:-nan%) 38284 + 0 with itself and mate mapped 331 + 0 singletons (0.83%:-nan%) 76 + 0 with mate mapped to a different chr 54 + 0 with mate mapped to a different chr (mapQ>=5)
This is what I get as part of GATK info stats when running RealignerTargetCreator:
INFO 14:42:05,815 MicroScheduler - 5175 reads were filtered out during traversal out of 276045 total (1.87%) INFO 14:42:05,816 MicroScheduler - -> 84 reads (0.03% of total) failing BadMateFilter INFO 14:42:05,816 MicroScheduler - -> 1014 reads (0.37% of total) failing DuplicateReadFilter INFO 14:42:05,816 MicroScheduler - -> 4077 reads (1.48% of total) failing MappingQualityZeroFilter
This is what I get as part of GATK info stats when running DepthOfCoverage (on the orignal BAM, not after realignment):
INFO 15:03:17,818 MicroScheduler - 2820 reads were filtered out during traversal out of 309863 total (0.91%) INFO 15:03:17,818 MicroScheduler - -> 1205 reads (0.39% of total) failing DuplicateReadFilter INFO 15:03:17,818 MicroScheduler - -> 1615 reads (0.52% of total) failing UnmappedReadFilter
Why are all of these so different? Why are there much more total reads and duplicate reads for GATK stats?
I was wondering if there is an option to remove duplicate reads when the coverage is determined using DepthOfCoverage from a .BAM file. Or is there an alternate way to remove the duplicate reads.