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Analysis Summary

2 sample(s) in this analysis: father mother
All 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: SAMtools
1 aligner(s) used: bwamem
File used for caculating coverage statistics and extracting variants: hg19_exome.bed
Readgroup : READGROUP_father,READGROUP_mother
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: 12
NOTICE: /tmp/12516295.hpc-pbs.hpcc.usc.edu will be used for storing temporary files
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FINAL OUTPUT for father:
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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.

father_result/father_bwamem.merge.0_samtools.extract.vcf
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FINAL OUTPUT for mother:
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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.

mother_result/mother_bwamem.merge.0_samtools.extract.vcf

Result highlights

father

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.


mother

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.



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