Skip to main content
. 2011 Aug 3;39(19):e132. doi: 10.1093/nar/gkr599

Table 2.

Comparison of SNP calling by CRISP, SAMtools, GATK and SNVer

Data No. of SNP
Ti/Tva
Concordanceb
All Known Novel dbSNP% All Known Novel TP/P (%)
Autism (pooled)
    Case
        CRISP 2182 1791 391 82.1 1.68 1.79 1.26 101/101 (100)
        SNVer 2182 1795 387 82.3 1.71 1.81 1.35 102/102 (100)
        SAMtools 261 260 1 99.6 2.26 2.29 0/1 16/16 (100)
    Control
        CRISP 2063 1610 453 78.0 1.68 1.83 1.27 96/96 (100)
        SNVer 2063 1617 446 78.4 1.78 1.89 1.45 95/95 (100)
        SAMtools 239 238 1 99.6 2.06 2.05 1/0 16/16 (100)
T1D (pooled)
    Case
        CRISP 306 93 213 30.3 0.95 2.58 0.63 N/A
        SNVer 306 126 180 41.2 1.71 2.15 1.47
        SAMtools 14 9 5 64.3 10/4 8/1 2/3
    Control
        CRISP 167 110 57 65.9 1.49 2.93 0.46
        SNVer 167 120 47 71.9 2.34 3.00 1.35
        SAMtools 18 12 6 66.7 14/4 11/1 3/3
ADHD (Individual)
    84 060
        SNVer 18 001 17 535 466 97.4 2.89 2.89 2.73 4158/4183 (99.4)
        SAMtools 48 988 47 513 1475 97.0 2.66 2.68 2.16 4437/8116 (54.7)
        SAMtools20× 15 038 14 538 500 96.7 2.70 2.72 2.11 2034/3158 (64.4)
        GATK 19 655 19 713 482 97.6 2.91 2.94 2.15 4649/4657 (99.8)
    84 615
        SNVer 17 436 16 914 522 97.0 2.85 2.87 2.22 4032/4063 (99.2)
        SAMtools 46 037 44 489 1548 96.6 2.64 2.67 1.94 4173/7643 (54.4)
        SAMtools20× 15 510 14 942 568 96.3 2.74 2.77 2.02 2062/3247 (63.5)
        GATK 18 892 18 419 473 97.5 2.89 2.92 2.03 4537/4566 (99.4)
    92 157
        SNVer 18 676 18 208 468 97.5 2.90 2.92 2.37 4192/4224 (99.2)
        SAMtools 49 729 47 693 2036 95.9 2.69 2.73 2.03 4251/7996 (53.2)
        SAMtools20× 15 881 15 370 511 96.8 2.80 2.83 1.99 2028/3259 (62.2)
        GATK 20 100 19 631 469 97.7 2.98 3.00 2.35 4700/4710 (99.8)

aTransition and transversion ratio for the identified variants. When the number of variants is small we just report the numbers but not calculate the ratio, e.g. 10/4 for all variants in T1D case by SAMtools means 10 transitions and 4 transversions.

bGenotype concordance. P represents the number of variants called by each program and also genotyped. TP represents the number of variant calls concordant between sequencing data and individual genotyping data.

20×: Additional filtering of sequencing depth ≥20 is applied.