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--- mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup [2015/04/02 13:53] – mkatari
+++ mkatari-bioinformatics-august-2013-bioinformatics-august-2013-mpileup [2015/11/18 19:48] (current) – mkatari
@@ Line 20: / Line 20: @@
   * remove duplicates
   * create a bam index for dedup bam files
+<code>
+bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam
+samtools view -bS Cohen.sam > Cohen.bam
+samtools sort Cohen.bam Cohen_sorted
+samtools index Cohen_sorted.bam
+</code>
 For further curation
@@ Line 35: / Line 43: @@
   * filter using vcfutils
   * index vcf file to visualize on IGV
 <code>
-bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam
+samtools mpileup -uf PTC_Human.fasta \
-samtools view -bS Cohen.sam > Cohen.bam
+         Cohen.bam \
-samtools sort
+         Linder.bam \
+         Rikhi.bam \
+         Sherman.bam > PTC_human.bcf
 </code>
+Run bcf tools to call the snps:
+  * b means save output as bcf
+  * v means output potential variant sites only
+  * c means call snps
+  * g call genotypes at variant sites.
+<code>
+bcftools view -bvcg PTC_human.bcf > PTC_human.raw.bcf &
+</code>