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I would read through the GATK website that describes what they recommend to do. You can also look up the "Exome Sequencing Manual" here, even if you don't have exome data. Those would be good starters. -
what sort of filters necessary before calling SNPs
I have a data 100XPE aligned with BWA using hg19 (I allowed gap= 3; alignment quality score> 90% ). I want to call SNPs. I belive before I can use GATK or other tools I need to filter sam/bam file after alignments. There are various parametrs mentioned For sure PCR duplicates; read fails vendor quality have to be used.Is there any other typical flag which can affect my SNP calling? I am using Samtools
Apology for a very basic question
Thanks
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