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I have Bisulfite- treated sequence mapped using Bismark and Bowtie2 and I'd like to call SNPs and INDELs from it. I have used Bis-SNP to call SNPs but it doesn't call indels , can I use GATK to call indels from the mapped data? Do u have any support to Bisulfite data?
Another question please, the data is a mix from 6 different people do u have any support fro pooled data?
Thanks for your help.