= 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 (for reads of at least 70 nt):
{{{
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 ==