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Old 04-28-2011, 12:39 AM   #1
gavin.oliver
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Default 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?
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Old 04-28-2011, 06:24 AM   #2
nilshomer
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Good question, see the Wiki: http://seqanswers.com/wiki/SEQanswers
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Old 04-28-2011, 06:28 AM   #3
GW_OK
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bwa, GATK, vcftools, samtools, picard, PLINK...

(Excel, grep... LOL)
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Old 04-30-2011, 10:35 AM   #4
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Thanks guys
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