Through vcftools I got a file(`my.var-final.vcf`, 27 MB) which contain in formation of SNPs and indels:

```
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) tha
n in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples
.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT my-sorted.bam
comp904_c0_seq1 30 . G T 73.5 . DP=4;VDB=0.0014;AF1=1;AC1=2;DP4=0,0,4,0;MQ=60;FQ=-39 GT:PL:GQ 1/1:106,
12,0:21
comp904_c0_seq1 37 . C T 52 . DP=4;VDB=0.0014;AF1=1;AC1=2;DP4=0,0,3,0;MQ=60;FQ=-36 GT:PL:GQ 1/1:84,9
,0:16
comp904_c0_seq1 41 . A T 64.3 . DP=6;VDB=0.0020;AF1=1;AC1=2;DP4=0,0,5,0;MQ=60;FQ=-42 GT:PL:GQ 1/1:97,1
5,0:27
comp904_c0_seq1 74 . A G 4.77 . DP=21;VDB=0.0147;AF1=0.4999;AC1=1;DP4=10,5,3,1;MQ=60;FQ=6.99;PV4=1,1.2e-06,1,1
GT:PL:GQ 0/1:33,0,255:33
comp904_c0_seq1 133 . G T 137 . DP=36;VDB=0.0404;AF1=0.5;AC1=1;DP4=2,3,19,10;MQ=60;FQ=33;PV4=0.35,1.6e-09,1,1
GT:PL:GQ 0/1:167,0,60:63
```

Is there any way to summarize this variation information, like some tools, scripts or something?
There are tons of tools that will give you what you want. Here is one: http://vcftools.sourceforge.net/documentation.html#file
