GATKvariantdiscovery.pdfVIP

Variant discovery – SNPs/InDels ● GATK – A suite of tools including local realigner, quality score recalibrator, and SNP/INDEL caller. ● SAMtools – SNPs and short INDELs Variant discovery – SNPs/INDELs ● GATK – A suite of tools including local realigner, quality score recalibrator, and SNP/INDEL caller. ● SAMtools – SNPs and short INDELs ● CRISP – Identify SNPs and INDELs from pooled NGS data ● SNVer – An operating system independent statistical tool for the identification of SNPs/INDELs GATK variant calling workflow /gatk//events/3093/GATKwh1-BP-0B-Intro_to_GATK.pdf Why duplicates are bad /gatk//events/3093/GATKwh1-BP-1-Map_and_Dedup.pdf Indel Realignment Several Consecutive “SNPs” only found on reads ending on the right of the homopolymer Several consecutive “SNPs” only found on reads ending on the left of the homopolymer /gatk//events/3093/GATKwh1-BP-2-Realignment.pdf Indel Realignment /gatk//events/3093/GATKwh1-BP-2-Realignment.pdf Indel Realignment ● Information used to carry out indel realignment – Known sites (dbSNP, 1000 Genomes) – Indels present in original alignments (in CIGARs) – Sites where evidence suggests a hidden indel Indel Realignment + Known sites ● Input BAM file not necessary if processing only at known indels ● Known indels speed up processing and improve accuracy, but is not required ● At indels seen in the original BAM is the recommended mode ● Only at known indels speed up processing, accurate for ~90-95% of indels ● Using full Smith-Waterman realignment is the most accurate, but has heavy computational cost and not really necessary with the new techs /gatk//events/3093/GATKwh1-BP-2-Realignment.pdf DePristo M., Banks E., Poplin R. et. al., A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Gen. Indel Realignment Venn diagrams showing the number of identified variants for tested germline (A), somatic (B), CNV (C) and exome CNV (D) tools. Pabinger S e