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SnpSift TsTv

Calculate transition/transversion ratios and other variant statistics per sample.

Usage

java -jar SnpSift.jar tstv file.vcf

Warning

Only SNPs are used for Ts/Tv calculations.

Output

The command outputs four statistics sections, all broken down per sample:

  • TS/TV stats: Transition and transversion counts and ratios per sample
  • Hom/Het stats: Homozygous reference, one ALT, two ALTs, and missing counts
  • Variant type stats: Counts by variant type (SNP, MNP, INS, DEL, MIXED, Multiallelic)
  • Allele count stats: Minor allele count distribution

Example:

java -jar SnpSift.jar tstv s.vcf

TS/TV stats:
Sample ,1,2,3,4,5,6,7,8,9,10,11,12,Total
Transitions ,150488,150464,158752,156674,152936,160356,152276,155314,156484,149276,151182,153468,1847670
Transversions ,70878,70358,73688,72434,70828,76150,72030,71958,72960,69348,70180,71688,862500
Ts/Tv ,2.123,2.139,2.154,2.163,2.159,2.106,2.114,2.158,2.145,2.153,2.154,2.141,2.142

Hom/Het stats:
...

Variant type stats:
...

Allele count stats:
...