Changes between Version 19 and Version 20 of SOPs/variant_calling

Timestamp:

07/18/17 08:14:47 (8 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -58 +58 @@
 == Call raw variants with mpileup+bcftools ==
 
-Call variants (one sample vs. reference) with samtools' mpileup+bcftools (see the [http://samtools.sourceforge.net/mpileup.shtml samtools' variant calling page] for more details).
+Call variants (one sample vs. reference) with samtools' mpileup+bcftools (see the [http://www.htslib.org/workflow/#mapping_to_variant samtools' variant calling workflow] for more details).
 In our experience, "-B" (disable BAQ) or "-E" (recalculate BAQ) works better than the default method, which can remove some obvious variants.
 {{{
@@ -71 +71 @@
 == Add filters and annotations to raw variants ==
 
-This step uses vcf-annotate from the [http://vcftools.sourceforge.net/docs.html VCFtools suite]
+This step uses vcf-annotate from the [https://vcftools.github.io/perl_module.html VCFtools suite]
 
 Annotate variants by adding tags ("filters" but all variants are kept) to each variant, using all default filters.