Hello,
I have some truseq cancer panel amplicon data and I am in process of calling Somatic variants in Tumor samples with MuTect. By using the default fraction_contamination, I am not getting any entries with "KEEP" status. However, reducing this does start yielding SNPs. I am not sure what will be the ideal value here, hence I have been trying to run ContEst with GATK 3.7 as suggested on the website. But, I am not getting any output. Here are the details of the command:
GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar -T ContEst -R hg19.fa -I:eval tumor_sorted.bam -I:genotype normal_sorted.bam --popfile popaf/hapmap_3.3_hg19_pop_stratified_af_sorted.vcf -isr INTERSECTION -o output.txt -L targets.bed
Here are the STDOUT and STDERR:
INFO 13:53:43,463 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:53:43,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
INFO 13:53:43,652 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 13:53:43,652 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 13:53:43,652 HelpFormatter - [Wed Apr 05 13:53:43 BST 2017] Executing on Linux 3.10.0-229.el7.x86_64 amd64
INFO 13:53:43,653 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_71-b15
INFO 13:53:43,656 HelpFormatter - Program Args: -T ContEst -R hg19.fa -I:eval tumor_sorted.bam -I:genotype normal_sorted.bam --popfile popaf/hapmap_3.3_hg19_pop_stratified_af_sorted.vcf -isr INTERSECTION -o output.txt -L targets.bed
INFO 13:53:43,892 HelpFormatter - Executing as urmi208@node6 on Linux 3.10.0-229.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_71-b15.
INFO 13:53:43,892 HelpFormatter - Date/Time: 2017/04/05 13:53:43
INFO 13:53:43,892 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:53:43,892 HelpFormatter - --------------------------------------------------------------------------------
INFO 13:53:43,905 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:53:44,787 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 13:53:44,794 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 13:53:44,973 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
INFO 13:53:45,491 IntervalUtils - Processing 38385 bp from intervals
INFO 13:53:46,311 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
INFO 13:53:46,390 GenomeAnalysisEngine - Done preparing for traversal
INFO 13:53:46,390 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 13:53:46,391 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 13:53:46,391 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 13:53:46,392 ContEst - Running in sequencing mode
INFO 13:54:08,909 ContEst - Total sites: 37742
INFO 13:54:08,910 ContEst - Population informed sites: 37
INFO 13:54:08,910 ContEst - Non homozygous variant sites: 32
INFO 13:54:08,910 ContEst - Homozygous variant sites: 5
INFO 13:54:08,910 ContEst - Passed coverage: 5
INFO 13:54:08,911 ContEst - Results: 0
INFO 13:54:08,913 ProgressMeter - done 68536.0 22.0 s 5.5 m 99.8% 22.0 s 0.0 s
INFO 13:54:08,914 ProgressMeter - Total runtime 22.52 secs, 0.38 min, 0.01 hours
INFO 13:54:08,914 MicroScheduler - 918 reads were filtered out during the traversal out of approximately 893918 total reads (0.10%)
INFO 13:54:08,914 MicroScheduler - -> 0 reads (0.00% of total) failing BadCigarFilter
INFO 13:54:08,915 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter
INFO 13:54:08,915 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 13:54:08,915 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 13:54:08,915 MicroScheduler - -> 918 reads (0.10% of total) failing NotPrimaryAlignmentFilter
INFO 13:54:08,915 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
Done. ------------------------------------------------------------------------------------------
There were no warn messages.
I seems that most things are filtered out as data is down sampled with target coverage of 1000. I will be grateful if you could provide any help.
Many thanks.
