Changes between Version 15 and Version 16 of SOPs/variant_calling

Timestamp:

01/11/16 14:23:50 (9 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -61 +61 @@
 In our experience, "-B" is needed to disable BAQ computation, which would otherwise remove many obvious variants.
 {{{
-samtools mpileup -d100000 -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
+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
 #in bcftools call: -m for multi-allelic, -c for bi-alleleic
 }}}
 Call variants (multiple sample vs. reference) using a set of BAM files
 {{{
-samtools mpileup -d100000 -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa *_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| ALL_reads.bt2.sorted_unique.raw.bcf
+samtools mpileup -d100000 -t DP,DPR,DV,DP4,INFO/DPR,SP -Buf /nfs/genomes/sgd_2010/bwa/sacCer3.fa *_reads.bt2.sorted_unique.bam | bcftools call -O b -v -c - >| ALL_reads.bt2.sorted_unique.raw.bcf
 }}}