Changes between Version 10 and Version 11 of SOPs/callingSNPs
- Timestamp:
- 01/16/14 16:09:53 (11 years ago)
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SOPs/callingSNPs
v10 v11 29 29 == Filtering SNPs == 30 30 31 * Remove, or retrieve, known SNPs 32 33 34 {{{ 35 #To remove known SNPs, use intersectBed (bedtools). Known SNPs can be downloaded from Ensembl or NCBI/UCSC (eg. dbSNP) 36 intersectBed -a accepted_hits.raw.filtered.vcf -b Mus_musculus.NCBIM37.60.bed -wo > filteredSNPs.vcf 37 }}} 38 31 * See [wiki:SOPs/variant_calling Add filters and annotations to raw variants]. 39 32 40 33 == Annotating SNPs ==