Analysis Summary

3 sample(s) in this analysis: father mother son
Multi-sample variant calling ENABLED, assume all samples in the same breed.
Input is exome (or captured) sequencing data.
3 variant caller(s) used: GATK_HaploTyperCaller SAMtools VarScan
1 aligner(s) used: bwamem
File used for caculating coverage statistics and extracting variants: hg19_exome.bed
Readgroup : READGROUP_father,READGROUP_mother,READGROUP_son
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: 8
Two INPUT files detected, PAIRED ends mode
Variant calling are run in parallel mode [EXPERIMENTAL].
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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.extract_consensus.vcf
father_result/father_bwamem.sort.rmdup.readfiltered.realn.recal_gatkhc.multi-call.filter.extract.vcf
father_result/father_bwamem.sort.rmdup.readfiltered_samtools.multi-call.filter.extract.vcf
father_result/father_bwamem.sort.rmdup.readfiltered_varscan.multi-call.filter.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.extract_consensus.vcf
mother_result/mother_bwamem.sort.rmdup.readfiltered.realn.recal_gatkhc.multi-call.filter.extract.vcf
mother_result/mother_bwamem.sort.rmdup.readfiltered_samtools.multi-call.filter.extract.vcf
mother_result/mother_bwamem.sort.rmdup.readfiltered_varscan.multi-call.filter.extract.vcf
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FINAL OUTPUT for son:
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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.
son_result/son.extract_consensus.vcf
son_result/son_bwamem.sort.rmdup.readfiltered.realn.recal_gatkhc.multi-call.filter.extract.vcf
son_result/son_bwamem.sort.rmdup.readfiltered_samtools.multi-call.filter.extract.vcf
son_result/son_bwamem.sort.rmdup.readfiltered_varscan.multi-call.filter.extract.vcf

Result highlights

father

There are 81093904 QC-passed reads.
72469565(89.36%) reads are mapped.
53.22% reads are mapped to target region.
Average coverage is 69.91 (in target region if this is captured sequencing).
29494 SNPs are called.
1690 indels are found.

mother

There are 71205444 QC-passed reads.
64073406(89.98%) reads are mapped.
61.07% reads are mapped to target region.
Average coverage is 63.76 (in target region if this is captured sequencing).
29411 SNPs are called.
1610 indels are found.

son

There are 138779950 QC-passed reads.
124428082(89.66%) reads are mapped.
52.49% reads are mapped to target region.
Average coverage is 113.44 (in target region if this is captured sequencing).
30157 SNPs are called.
1740 indels are found.

Details can be found on each SAMPLE page.