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-   -   Most commonly used tools (http://seqanswers.com/forums/showthread.php?t=11005)

gavin.oliver 04-28-2011 12:39 AM

Most commonly used tools
 
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 04-28-2011 06:24 AM

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

GW_OK 04-28-2011 06:28 AM

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

(Excel, grep... LOL)

gavin.oliver 04-30-2011 10:35 AM

Thanks guys :)


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