Hello everybody,
I’m just starting to analyze mouse exome. I got mouse exome fastq files (SRR519332) looks like Agilent SureSelect mouse all exon v1 from DRA/SRA/ERA.
Using the exome target file (S0276129_Covered.bed, 50Mb) from Agilent SureDesign, I called SNP/InDel by GATK 1.6 and AvadisNGS 1.4.6. Both of programs yielded about 6,000 variants and matching rate was about 80%. Average read depth of coverage on the target region was about 70 by GATK’s DepthOfCoverage.
Is the number of variants reasonable?
When I analyzed human exome (SureSelect All human 50Mb) I got about 50,000 variants. The number of variants from mouse exome looks very small compare than human.
Thank you.
I’m just starting to analyze mouse exome. I got mouse exome fastq files (SRR519332) looks like Agilent SureSelect mouse all exon v1 from DRA/SRA/ERA.
Using the exome target file (S0276129_Covered.bed, 50Mb) from Agilent SureDesign, I called SNP/InDel by GATK 1.6 and AvadisNGS 1.4.6. Both of programs yielded about 6,000 variants and matching rate was about 80%. Average read depth of coverage on the target region was about 70 by GATK’s DepthOfCoverage.
Is the number of variants reasonable?
When I analyzed human exome (SureSelect All human 50Mb) I got about 50,000 variants. The number of variants from mouse exome looks very small compare than human.
Thank you.
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