1 / 12

GATK assessment follow up

GATK assessment follow up. Jianying Li. Samples tested. Analytical parameter set up. Aligner: BWA 0.5.9 Samtools : 0.1.12a GATK: 1.0.5083 Covariates: readgroup * , Q raw , dinucleotide, machine cycle SVA version: 1.1. Reported quality score (als9c2, build 37).

nasya
Download Presentation

GATK assessment follow up

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. GATK assessment follow up Jianying Li

  2. Samples tested

  3. Analytical parameter set up • Aligner: BWA 0.5.9 • Samtools: 0.1.12a • GATK: 1.0.5083 • Covariates: readgroup*, Qraw, dinucleotide, machine cycle • SVA version: 1.1

  4. Reported quality score (als9c2, build 37) 15% more bases with Q32 and above Before recalibration After recalibration

  5. Computational complexity Processed BAM files ~ 4 days SNVs & Indel files var_flt_vcf.snp var_flt_vcf.indel ~ 6 hours SNV count Hom/het ratio Indel count Ti/Tv ratio Overlap with dbSNP concordance Het/tot ratio on X

  6. Increased variant calls (als9c2)

  7. Ratio (%) of variant calls --GATK against raw

  8. Ti/Tv ratio (??)

  9. Reduced overlap to dbsnp

  10. Increased concordance (SVA) Dukscz0106, build 36

  11. Increased concordance (SVA) als9c2, build 37

  12. Decreased concordance (??) mchd002A2, build 36

More Related