Helmholtz Zentrum München Helmholtz Zentrum München Institute of Human GeneticsInstitute of Human Genetics10.07.2012 10.07.2012

Institute of Human Genetics

Variant Calling

Methods

SamtoolsMultisample Variant Calling

SamtoolsMultisample Variant Calling

HG00117Lab1 BAM

HG00117Lab2 BAM

HG00117Lab3 BAM

HG00117Lab4 BAM

HG00117Lab5 BAM

HG00117Lab6 BAM

HG00117Lab7 BAM

HG00117Lab1 BAM

HG00117Lab2 BAM

HG00117Lab3 BAM

HG00117Lab4 BAM

HG00117Lab5 BAM

HG00117Lab6 BAM

HG00355Lab7 BAM

HG00117Lab1 BAM

HG00117Lab2 BAM

HG00117Lab3 BAM

HG00117Lab4 BAM

HG00117Lab5 BAM

HG00117Lab6 BAM

NA06986Lab7 BAM

HG00117Lab1 BAM

HG00117Lab2 BAM

HG00117Lab3 BAM

HG00117Lab4 BAM

HG00117Lab5 BAM

HG00117Lab6 BAM

NA19095Lab7 BAM

HG00117Lab1 BAM

HG00117Lab2 BAM

HG00117Lab3 BAM

HG00117Lab4 BAM

HG00117Lab5 BAM

HG00117Lab6 BAM

NA20527Lab7 BAM

Comparison with 1000G data

• Filtering of 1000G Variants:

• Gencode v12 Transcripts

• Covered by at least one read in corresponding BAM files

• Comparison of VCF files with custom Perl script

• Output:

• matching.vcf

• not_matching.vcf

• not_found.vcf

Comparison with 1000G data

Sample CorrectGTs WrongGTs NotFoundGTs

HG00117 146911 18932 2692240

HG00355 146192 20208 2691683

NA06986 141685 20138 2696260

NA19095 134587 25872 2697624

NA20527 147888 18632 2691563

Comparison with 1000G data

CorrectGTs NotFoundGTs

number of reads number of reads

Methods

…

SamtoolsMultisample Variant Calling

SamtoolsMultisample Variant Calling

HG00117Lab1 BAM

HG00355Lab1 BAM

NA06986Lab1 BAM

NA19095Lab1 BAM

NA20527Lab1 BAM

SamtoolsMultisample Variant Calling

SamtoolsMultisample Variant Calling

HG00117Lab2 BAM

HG00355Lab2 BAM

NA06986Lab2 BAM

NA19095Lab2 BAM

NA20527Lab2 BAM

SamtoolsMultisample Variant Calling

SamtoolsMultisample Variant Calling

HG00117Lab3 BAM

HG00355Lab3 BAM

NA06986Lab3 BAM

NA19095Lab3 BAM

NA20527Lab3 BAM

Known RNA editing sites

chrom position gene % readsoverlap with

1000G coverage

chr4 158257875 GRIA2 0 no 0

chr4 158281294 GRIA2 0 no 0

chr4 57976234 IGFBP7 0 no 0

chr4 57976286 IGFBP7 0 no 1

chr5 156736808 CYFIP2 0 no 6573

chr11 105804694 GRIA4 0 no 1

chr12 5021742 KCNA1 0 no 31

chr20 36147533 BLCAP 0 no 2365

chr20 36147563 BLCAP 0 no 1930

chr20 36147572 BLCAP 16% no 1829

chr21 30953750 GRIK1 0 no 24

chrX 122598962 GRAI3 67% ? 3

chrX 151358319 GABRA3 0 ? 19939

chrX 153579950 FLNA 0 ? 0

Li et al., Science, 2009

Future work

• Multi Sample calling on all GEM BAM files

• Systematic analysis of not_found/not_matching calls

• Comparison with imputation data (and future phase 2 data)

• Systematik calling of RNA editing sites (e.g. Ramaswami et al., Nature Methods, 2012)