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2 sample(s) in this analysis: father motherAll input is merged on a per-sample basis (after alignment if FASTQ).Multi-sample variant calling DISABLED.Input is exome (or captured) sequencing data.1 variant caller(s) used: SAMtools1 aligner(s) used: bwamemFile used for caculating coverage statistics and extracting variants: hg19_exome.bedReadgroup : READGROUP_father,READGROUP_motherLibrary : LIBRARYSequencing platform: ILLUMINAReference genome build is hg19dbsnp138 is used for variant calling and recalibration (in GATK VQSR).Java memory usage is limited to 1750mMax number of processes: 12NOTICE: /tmp/12516295.hpc-pbs.hpcc.usc.edu will be used for storing temporary files###################################################FINAL OUTPUT for father:###################################################NOTICE: Both consensus results and individual results are listed.WARNING: consensus results may not be available because some variant callers or aligners may fail to generate output.father_result/father_bwamem.merge.0_samtools.extract.vcf###################################################FINAL OUTPUT for mother:###################################################NOTICE: Both consensus results and individual results are listed.WARNING: consensus results may not be available because some variant callers or aligners may fail to generate output.mother_result/mother_bwamem.merge.0_samtools.extract.vcf
There are 3992668 QC-passed reads.3575179(89.54%) reads are mapped. 53.28% reads are mapped to target region.Average coverage is 3.66 (in target region if this is captured sequencing).3203 SNVs are called.66 indels are found.
There are 3979773 QC-passed reads.3581498(89.99%) reads are mapped. 61.13% reads are mapped to target region.Average coverage is 4.22 (in target region if this is captured sequencing).4126 SNVs are called.111 indels are found.
Details can be found on each SAMPLE page.