VCF format viewer

[Guigra]

I call SNPs and short INDELs with samtools. Now I need a program to open my output to VCF, and also to give me some results as number of SNPs and indels, for example.

Does anyone use or know a good software to do this?

Tanks.

[chadn737]

Do you mean "write" the output to VCF? If you used samtools, then they tell you exactly how to obtain a VCF file using bcftools view.

http://samtools.sourceforge.net/mpileup.shtml

[Guigra]

Exactly. Expressed myself badly ... I used samtools and bcftools ... My exit was in VCF. Now I need a software to read the outputs and I data as number of SNPs, indels...

To call SNPs and short INDELs I used this commands lines:
samtools mpileup -uf ref.fa aln1.bam aln2.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -D100 > var.flt.vcf

[GenoMax]

vcftools: http://vcftools.sourceforge.net/

If you want to visualize the vcf files you can use IGV from Broad: http://www.broadinstitute.org/igv/viewing_vcf_files

[swbarnes2]

.vcf format is plain text. You can look at it in anything. Just throw it in Excel.