Most commonly used tools

[gavin.oliver]

Hi,

I'm just looking for the names of some tools commonly used in analysing human genomic resequencing data for SNPs/Indels etc?

I've seen repeated mention of aligning with bowtie and snp calling with SAMtools - are there any other common ones?

[nilshomer]

Good question, see the Wiki: http://seqanswers.com/wiki/SEQanswers

[GW_OK]

bwa, GATK, vcftools, samtools, picard, PLINK...

(Excel, grep... LOL)

[gavin.oliver]

Thanks guys