Changes between Initial Version and Version 1 of SOPs/variant_calling

Timestamp:

10/15/13 13:56:42 (11 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ +1 @@
+
+= Variant calling and analysis =
+
+The main steps comprising variant calling and analysis are
+* mapping short reads
+* calling raw variants
+* filtering (really more like 'tagging') variants
+* annotating variants
+
+== Map short reads ==
+
+After quality control and/or filtering of reads...
+
+Single reads with bowtie2:
+{{{
+bowtie2 -x /nfs/genomes/sgd_2010/bowtie/sacCer3 A_reads.fq -S A_reads.bt2.sam
+}}}
+
+Single reads with bwa:
+{{{
+bwa aln /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.fq > A_reads.sai
+bwa samse /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.sai  A_reads.fq > A_reads.bwa.sam
+}}}
+
+Paired-end reads with bowtie2:
+{{{
+bowtie2 -x /nfs/genomes/sgd_2010/bowtie/sacCer3 -1 A_reads.1.fq -2 A_reads.2.fq -S A_reads.1+2.bt2.sam
+}}}
+
+Paired-end reads with bwa:
+{{{
+bwa mem /nfs/genomes/sgd_2010/bwa/sacCer3.fa A_reads.1.fq A_reads.2.fq > A_reads.1+2.bwa.sam
+}}}
+
+Convert to BAM, sort, and index [with a custom BaRC script that uses samtools]:
+{{{
+/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl A_reads.bwa.sam
+}}}
+
+Get uniquely mapping reads
+{{{
+samtools view -h A_reads.bt2.bam | grep -v XS:i: | samtools view -bS - > A_reads.bt2.sorted_unique.bam
+}}}
+
+== Call raw variants ==