Changes between Version 16 and Version 17 of SOPs/variant_calling

Timestamp:

07/20/16 08:30:23 (9 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).
-In our experience, "-B" is needed to disable BAQ computation, which would otherwise remove many obvious variants.
+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).
+In our experience, "-B" (disable BAQ) or "-E" (recalculate BAQ) works better than the default method, which can remove some obvious variants.
 {{{
 samtools mpileup -d100000 -t DP,DPR,DV,DP4,INFO/DPR,SP -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| A_reads.bt2.sorted_unique.raw.bcf