someone solve my problem which is that i am using galaxy cloud base server analysis. i completed alignment by BWA and Mpileup is also over. after mpileup i got VCF file. but from VCF file how can i count SNP and INDEL ? please someone solve the my problem. thank you all
Do you have GATK installed in your galaxy server? If so there is a module as
-SelectVariants with handle
-selectType, they can easily take input your raw vcf and compartment them in 2 vcf files one having INDELS and another having SNPs when you use the module and put the
-selectType [SNP/INDEL]. Alternatively you can always post your galaxy related queries here, since the user is quite active. @Jennifer Hillman Jackson is very much active there to address to your queries. Alternatively you can install GATK latest version and use the handles above and do the operations or follow this link where you can use other tools outside of galaxy as well.
Then there is master @Pierre tools which you can use externally on your vcf file to perform the operations outside galaxy as well. Here is the thread.
Search a bit more in google and hit for your query will come. Do not restrict yourself just to one tool. Programmatic usage is always beneficial and you can push yourself a bit to learn few command line tricks.