Analysis Summary

1 sample(s) in this analysis: example
Input is exome (or captured) sequencing data.
4 variant caller(s) used: GATKLite_UnifiedGenotyper SAMtools FreeBayes Consensus
1 aligner(s) used: bwamem
Variants shared by at least 2 combinations of aligners and callers are printed.
File used for caculating coverage statistics and extracting variants: hg19_exome.bed
Readgroup : READGROUP_example
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 example:
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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.
example_result/example.extract_consensus.vcf
example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf
example_result/example.0_bwamem.sort.rmdup.readfiltered.0_samtools.extract.vcf
example_result/example.0_bwamem.sort.rmdup.readfiltered.0_freebayes.extract.vcf

Result highlights

example

There are 294058 QC-passed reads.
201139(68.40%) reads are mapped.
12.83% reads are mapped to target region.
Average coverage is 0.04 (in target region if this is captured sequencing).
52 SNVs are called.
2 indels are found.

Details can be found on each SAMPLE page.