Analysis Summary

1 sample(s) in this analysis: PatientXsomatic
Somatic mutation calling mode
Input is exome (or captured) sequencing data.
1 variant caller(s) used: VarScan
1 aligner(s) used: bwamem
File used for caculating coverage statistics and extracting variants: somatic_calling.bed
Readgroup : PATIENTX_PatientXsomatic
Library : LIBRARY
Sequencing platform: ILLUMINA
Reference genome build is hg19
dbsnp138 is used for variant calling and recalibration (in GATK VQSR).
Java memory usage is limited to 1750m
Max number of processes: 4
NOTICE: /tmp will be used for storing temporary files
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FINAL OUTPUT for PatientXsomatic:
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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.

PatientXsomatic_result/PatientXsomatic.0_bwamem.sort.readfiltered.0_varscan.somatic-call.extract.vcf

Result highlights

PatientXsomatic

There are 458754 QC-passed reads.
347409(75.73%) reads are mapped.
41.59% reads are mapped to target region.
Average coverage is 42.59 (in target region if this is captured sequencing).
178 SNVs are called.
21 indels are found.

Details can be found on each SAMPLE page.