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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 19:25] – mkatari
@@ Line 43: / Line 43: @@
 </code>
+<code>
+samtools mpileup -uf PTC_Human.fasta \
+         Cohen.bam \
+         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>